mummer-help — For general MUMmer questions and help.

[MUMmer-help] Installation help

[<ra...@bi...>]

Hi,
I am Ramya and i am new to this tool. I am not so good at command line usage but followed the commands specified in the tool for installation. I did find an error while installing the tool. it says no g++ GNU compiler found. When i am trying to install g++ it is showing some errors. Can you please help me out with this?
 
Regards,
Ramya

Re: [MUMmer-help] Exact alignment of contigs to a reference

[Adam P. <aph...@gm...>]

Hi Ruth,
Unfortunately there is not an easy way to do this. The location of the
alignment gaps is contained in the .delta file, which you could parse to
create your mapping (the file format is described in the manual). Other
alternatives: If you only care about difference positions, the show-snps
program will report all SNPs and Indels w/ coordinates in both sequences.
Or the show-aligns will dump a textual alignment representation which you
could also parse.

Best,
-Adam


On Tue, May 5, 2015 at 4:59 PM, Miller, Ruth <Rut...@bc...> wrote:

> Hi,
>
> I have used NUCmer to align contigs I have generated from next-generation
> sequencing data to a reference.
>
> I would like to create a dictionary which contains the position of every
> base in the query contigs in the reference. I hoped I might be able to do
> this using the .coords file, however, although you can tell the start and
> end of every contig compared to the reference, it does not provide the
> positions of the gaps, so you cannot tell the exact alignment of each
> position in the query contig compared to the reference.
> Is there any way to get the exact details of the alignment using
> NUCmer/MUMmer, from which I could parse the 1:1 relationship of every
> position in the query contigs compared to the reference?
>
> Thanks,
>
> Ruth
>
>
> ------------------------------------------------------------------------------
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>
>

[MUMmer-help] Exact alignment of contigs to a reference

[Miller, R. <Rut...@bc...>]

Hi,

I have used NUCmer to align contigs I have generated from next-generation sequencing data to a reference.

I would like to create a dictionary which contains the position of every base in the query contigs in the reference. I hoped I might be able to do this using the .coords file, however, although you can tell the start and end of every contig compared to the reference, it does not provide the positions of the gaps, so you cannot tell the exact alignment of each position in the query contig compared to the reference.
Is there any way to get the exact details of the alignment using NUCmer/MUMmer, from which I could parse the 1:1 relationship of every position in the query contigs compared to the reference?

Thanks,

Ruth

[MUMmer-help] Controlling core usage

[Ramesh k. R. <ram...@gm...>]

Hello,

Is it possible to assign number of cores to nucmer or mummer?

Thanks
Ramesh

Re: [MUMmer-help] ERROR: mummer and/or mgaps returned non-zero

[Ramesh k. R. <ram...@gm...>]

Hi Adam,
It worked! Thank you, you saved me..

Ramesh

On Wed, Apr 29, 2015 at 10:58 AM, Adam Phillippy <aph...@gm...>
wrote:

> Hi,
> The size of your reference sequence is larger than is supported by
> default. You can either break your reference into multiple files and run
> each individually, or recompile the mummer package with:
>
> > make clean
> > make CPPFLAGS="-O3 -DSIXTYFOURBITS"
>
>
> To increase maximum reference size permitted.
>
> Best,
> -Adam
>
>
> On Tue, Apr 28, 2015 at 10:18 PM, Ramesh krishnan Ramasamy <
> ram...@gm...> wrote:
>
>> Hi everyone,
>> I'm consistently getting following error while running both nucmer and
>> mummer.
>>
>> $ nucmer -maxmatch -c 100 -p nucmer ../reference.fasta ../query.fa
>> 1: PREPARING DATA
>> 2,3: RUNNING mummer AND CREATING CLUSTERS
>> # reading input file "nucmer.ntref" of length 712946597
>> # construct suffix tree for sequence of length 712946597
>> # (maximum reference length is 536870908)
>> # (maximum query length is 4294967295)
>> # process 7129465 characters per dot
>> /usr/bin/mummer: suffix tree construction failed: textlen=712946597
>> larger than maximal textlen=536870908
>> ERROR: mummer and/or mgaps returned non-zero
>>
>> To test myself, I simply pulled out few contigs from the reference genome
>> and used as query sequence. Unfortunately, I'm still running into the same
>> error.
>>
>> I appreciate any kind of help.
>>
>> Thanks
>> Ramesh
>>
>>
>> ------------------------------------------------------------------------------
>> One dashboard for servers and applications across Physical-Virtual-Cloud
>> Widest out-of-the-box monitoring support with 50+ applications
>> Performance metrics, stats and reports that give you Actionable Insights
>> Deep dive visibility with transaction tracing using APM Insight.
>> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li...
>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>>
>

Re: [MUMmer-help] ERROR: mummer and/or mgaps returned non-zero

[Adam P. <aph...@gm...>]

Hi,
The size of your reference sequence is larger than is supported by default.
You can either break your reference into multiple files and run each
individually, or recompile the mummer package with:

> make clean
> make CPPFLAGS="-O3 -DSIXTYFOURBITS"


To increase maximum reference size permitted.

Best,
-Adam


On Tue, Apr 28, 2015 at 10:18 PM, Ramesh krishnan Ramasamy <
ram...@gm...> wrote:

> Hi everyone,
> I'm consistently getting following error while running both nucmer and
> mummer.
>
> $ nucmer -maxmatch -c 100 -p nucmer ../reference.fasta ../query.fa
> 1: PREPARING DATA
> 2,3: RUNNING mummer AND CREATING CLUSTERS
> # reading input file "nucmer.ntref" of length 712946597
> # construct suffix tree for sequence of length 712946597
> # (maximum reference length is 536870908)
> # (maximum query length is 4294967295)
> # process 7129465 characters per dot
> /usr/bin/mummer: suffix tree construction failed: textlen=712946597 larger
> than maximal textlen=536870908
> ERROR: mummer and/or mgaps returned non-zero
>
> To test myself, I simply pulled out few contigs from the reference genome
> and used as query sequence. Unfortunately, I'm still running into the same
> error.
>
> I appreciate any kind of help.
>
> Thanks
> Ramesh
>
>
> ------------------------------------------------------------------------------
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] ERROR: mummer and/or mgaps returned non-zero

[Ramesh k. R. <ram...@gm...>]

Hi everyone,
I'm consistently getting following error while running both nucmer and
mummer.

$ nucmer -maxmatch -c 100 -p nucmer ../reference.fasta ../query.fa
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "nucmer.ntref" of length 712946597
# construct suffix tree for sequence of length 712946597
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 7129465 characters per dot
/usr/bin/mummer: suffix tree construction failed: textlen=712946597 larger
than maximal textlen=536870908
ERROR: mummer and/or mgaps returned non-zero

To test myself, I simply pulled out few contigs from the reference genome
and used as query sequence. Unfortunately, I'm still running into the same
error.

I appreciate any kind of help.

Thanks
Ramesh

Re: [MUMmer-help] problem with mummerplot / gnuplot

[Adam P. <aph...@gm...>]

Hi,
Probably a gnuplot 5 compatibility issue. I've added this to the bug
tracker. Gnuplot v4 is currently recommended for mummer, I have not tested
with v5.

Best,
-Adam


On Wed, Apr 22, 2015 at 11:01 AM, Adriaan Vanheule <
Adr...@ug...> wrote:

> Hi all,
>
>
>
> I am aligning genomes with MUMmer installed on Cygwin, running on my
> Windows 64 bit laptop. The NUCmer and delta-filter steps work fine, but I
> run into problems when I try to run mummerplot. Regardless of the options I
> use (--png, default), I get the following errors:
>
>
>
> gnuplot 5.0 patchlevel 0
>
> Writing filtered delta file out.filter
>
> Reading delta file out.delta.m
>
> Writing plot files out.fplot, out.rplot
>
> Writing gnuplot script out.gp
>
> Rendering plot out.png
>
>
>
> set mouse clipboardformat "[%.0f, %.0f]"
>
>           ^
>
> "out.gp", line 27: wrong option
>
>
>
> WARNING: Unable to run 'gnuplot out.gp',
>
>
>
> This seems like it could be more a gnuplot error than a mummerplot error,
> but I thought I would give it a try anyway. Does anyone know how I could
> resolve this?
>
>
>
> Kind regards
>
> Adriaan
>
>
> ------------------------------------------------------------------------------
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live
> exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
> event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

Re: [MUMmer-help] Aligning a 30 Mb scaffold to a 3 Gb Reference

[Adam P. <aph...@gm...>]

Hi Sanjit,
The best parameters depend on how related your scaffold is to the reference
assembly (same genome / species?) and how fragmented your contigs are.
Nucmer will not align through large stretches of N's, so if your scaffold
consists of a fasta file with contigs separated by N's, you will get
fragmented alignments as a result. As I suggested previously, I would run
delta-filter to select the best alignments for your scaffold versus the
reference genome. Then, from inspecting the coordinates of the remaining
matches you should be able to determine the extents of your scaffold mapped
to the reference.

-c 100 is relatively small, so for a 3GB genome, you will get a large
number of repeat-induced matches. If you are dealing with the same species,
I would increase -l to 50, and -c to your minimum contig size (say between
1000 or 5000), and increase the -g parameter to a few hundred.

Best,
-Adam


On Mon, Apr 27, 2015 at 1:32 PM, Sanjit Singh Batra <san...@gm...>
wrote:

> Hi!
>
> I asked this question as a response to the show-tilling thread, as you
> suggested. Although they are unrelated, it would be great to hear any
> suggestions from you regarding this. Any help with this problem will
> greatly reduce my computational off-time.
>
> Thanks again!
> sanjit
>
> On Tue, Apr 21, 2015 at 10:31 AM, Adam Phillippy <aph...@gm...>
> wrote:
>
>> Hi,
>> I see I picked up a separate question you had regarding show-tiling,
>> happy to answer questions in that more recent thread if you have further
>> questions.
>>
>> Best,
>> -Adam
>>
>>
>> On Fri, Apr 10, 2015 at 5:00 AM, Sanjit Singh Batra <
>> san...@gm...> wrote:
>>
>>> Hey!
>>>
>>> I have a 30Mb scaffold that was assembled using optical maps. I would
>>> like to align it to a 3Gb long reference assembly. Given the method through
>>> which this scaffold was constructed, it should align to a region in the
>>> reference, roughly the same size as itself.
>>>
>>> I am currently running nucmer with the -c 100 flag, and I get a very
>>> large number of fragmented alignments, the longest of which is under 1Mb.
>>> Is there any way I can alter the flags to get a larger, less fragmented
>>> alignment, for this particular case?
>>>
>>> Any suggestions are appreciated. Thanks!
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
>>> Develop your own process in accordance with the BPMN 2 standard
>>> Learn Process modeling best practices with Bonita BPM through live
>>> exercises
>>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
>>> event?utm_
>>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
>>> _______________________________________________
>>> MUMmer-help mailing list
>>> MUM...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>>
>>>
>>
>

[MUMmer-help] problem with mummerplot / gnuplot

[Adriaan V. <Adr...@UG...>]

Hi all,

I am aligning genomes with MUMmer installed on Cygwin, running on my Windows 64 bit laptop. The NUCmer and delta-filter steps work fine, but I run into problems when I try to run mummerplot. Regardless of the options I use (--png, default), I get the following errors:

gnuplot 5.0 patchlevel 0
Writing filtered delta file out.filter
Reading delta file out.delta.m
Writing plot files out.fplot, out.rplot
Writing gnuplot script out.gp
Rendering plot out.png

set mouse clipboardformat "[%.0f, %.0f]"
          ^
"out.gp", line 27: wrong option

WARNING: Unable to run 'gnuplot out.gp',

This seems like it could be more a gnuplot error than a mummerplot error, but I thought I would give it a try anyway. Does anyone know how I could resolve this?

Kind regards
Adriaan

Re: [MUMmer-help] Show-tiling: Switching the Reference and Query in a delta file

[Sanjit S. B. <san...@gm...>]

Hey!

I have a 30Mb scaffold that was assembled using optical maps. I would like
to align it to a 3Gb long reference assembly. Given the method through
which this scaffold was constructed, it should align to a region in the
reference, roughly the same size as itself.

I am currently running nucmer with the -c 100 flag, and I get a very large
number of fragmented alignments, the longest of which is under 1Mb. Is
there any way I can alter the flags to get a larger, less fragmented
alignment, for this particular case?

Any suggestions are appreciated. Thanks!

On Tue, Apr 21, 2015 at 10:25 AM, Adam Phillippy <aph...@gm...>
wrote:

> Hi Sanjit,
> There is no easy way to switch the reference and query once the alignment
> is computed.
>
> What do you intend to use show-tiling for? The 'delta-filter' program can
> be more flexible and useful for some tasks. If you run 'delta-filter -r' it
> will select the best alignments for each of your smaller reference
> sequences mapped to the larger query. If you run 'delta-filter -q' it will
> select the best alignment covering each region of your large query, which
> will (in effect) be similar to a tiling path of the best reference
> alignments across the query.
>
> Hope this helps,
> -Adam
>
>
> On Tue, Apr 14, 2015 at 9:45 PM, Sanjit Singh Batra <
> san...@gm...> wrote:
>
>> Hey!
>>
>> As mentioned in the manual, I switched the reference and the query while
>> using nucmer, since the reference was very large, and much larger than the
>> query. Now, I would like to run the show-tiling module on the resulting
>> delta file(This feature was the primary reason I started using mummer).
>> However, since the reference and query are switched, it tiles the reference
>> chromosomes over contigs, which is not what is desired.
>>
>> So, is there a script that can switch the reference and the query in a
>> delta file?
>>
>> Any suggestions are greatly appreciated. Thanks for your time!
>>
>>
>> ------------------------------------------------------------------------------
>> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
>> Develop your own process in accordance with the BPMN 2 standard
>> Learn Process modeling best practices with Bonita BPM through live
>> exercises
>> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
>> event?utm_
>> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
>> _______________________________________________
>> MUMmer-help mailing list
>> MUM...@li...
>> https://lists.sourceforge.net/lists/listinfo/mummer-help
>>
>>
>

Re: [MUMmer-help] Show-tiling: Switching the Reference and Query in a delta file

[Adam P. <aph...@gm...>]

Hi Sanjit,
There is no easy way to switch the reference and query once the alignment
is computed.

What do you intend to use show-tiling for? The 'delta-filter' program can
be more flexible and useful for some tasks. If you run 'delta-filter -r' it
will select the best alignments for each of your smaller reference
sequences mapped to the larger query. If you run 'delta-filter -q' it will
select the best alignment covering each region of your large query, which
will (in effect) be similar to a tiling path of the best reference
alignments across the query.

Hope this helps,
-Adam


On Tue, Apr 14, 2015 at 9:45 PM, Sanjit Singh Batra <san...@gm...>
wrote:

> Hey!
>
> As mentioned in the manual, I switched the reference and the query while
> using nucmer, since the reference was very large, and much larger than the
> query. Now, I would like to run the show-tiling module on the resulting
> delta file(This feature was the primary reason I started using mummer).
> However, since the reference and query are switched, it tiles the reference
> chromosomes over contigs, which is not what is desired.
>
> So, is there a script that can switch the reference and the query in a
> delta file?
>
> Any suggestions are greatly appreciated. Thanks for your time!
>
>
> ------------------------------------------------------------------------------
> BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
> Develop your own process in accordance with the BPMN 2 standard
> Learn Process modeling best practices with Bonita BPM through live
> exercises
> http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual-
> event?utm_
> source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>
>

[MUMmer-help] Show-tiling: Switching the Reference and Query in a delta file

[Sanjit S. B. <san...@gm...>]

Hey!

As mentioned in the manual, I switched the reference and the query while
using nucmer, since the reference was very large, and much larger than the
query. Now, I would like to run the show-tiling module on the resulting
delta file(This feature was the primary reason I started using mummer).
However, since the reference and query are switched, it tiles the reference
chromosomes over contigs, which is not what is desired.

So, is there a script that can switch the reference and the query in a
delta file?

Any suggestions are greatly appreciated. Thanks for your time!

[MUMmer-help] Aligning a 30 Mb scaffold to a 3 Gb Reference

[Sanjit S. B. <san...@gm...>]

Hey!

I have a 30Mb scaffold that was assembled using optical maps. I would like
to align it to a 3Gb long reference assembly. Given the method through
which this scaffold was constructed, it should align to a region in the
reference, roughly the same size as itself.

I am currently running nucmer with the -c 100 flag, and I get a very large
number of fragmented alignments, the longest of which is under 1Mb. Is
there any way I can alter the flags to get a larger, less fragmented
alignment, for this particular case?

Any suggestions are appreciated. Thanks!

Re: [MUMmer-help] help

[Adam P. <am...@um...>]

Hello Hui,
For mapping contigs to a chromosome, I typically suggest delta-filter -q.
That will filter based on an alignment score that is computed as (length *
identity) to identify the best alignments for each contig.

Have you overcome your problems running the delta-filter program?

Best,
-Adam


On Fri, Apr 3, 2015 at 3:18 AM, che...@ge... <
che...@ge...> wrote:

> Dear sir,
>
> Good days for you.
>
> Sorry to trouble you, however, we meet problem when we used nucmer.
>
> We want to link the contig into chromsome basing on finished genome. Then
> we run nucmer packages of mumer.
> After aligning,  It is so hard for us to choose a standard to filter the
> alignment (Coverage or aligning length ???)
>
> Would you like to give us some suggestions?
>
> many thanks for your help
> best regards
> yours sincerely, hui
>
>
> ------------------------------
> *----------------*
> Junhui Chen
> BGI TECH
> *Tel: +86-131-2890-7008 <%2B86-131-2890-7008> *
> *QQ: 751962963 *
> *Email: che...@ge... <http://chenjunhui@genomics.cn>*
> Main Building 10F│Beishan Industrial Zone│Yantian District│Shenzhen 518083
> │China
>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
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> things parallel software development, from weekly thought leadership blogs
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>
>

[MUMmer-help] help

[<che...@ge...>]

Dear sir,
Good days for you.
Sorry to trouble you, however, we meet problem when we used nucmer.
We want to link the contig into chromsome basing on finished genome. Then we run nucmer packages of mumer.After aligning, ?It is so hard for us to choose a standard to filter the alignment (Coverage or aligning length ???)
Would you like to give us some suggestions?
many thanks for your helpbest regardsyours sincerely, hui?



----------------Junhui ChenBGI TECHTel: +86-131-2890-7008?QQ: 751962963?Email:?che...@ge... Building 10F│Beishan Industrial Zone│Yantian District│Shenzhen 518083│China?

Re: [MUMmer-help] Fw: confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6

[<che...@ge...>]

confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6


----------------Junhui ChenBGI TECHTel: +86-131-2890-7008 QQ: 751962963 Email: che...@ge... Building 10F│Beishan Industrial Zone│Yantian District│Shenzhen 518083│China 
 From: che...@ge...: 2015-04-01 18:51To: mummer-helpSubject: Fw: Re: confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6




----------------Junhui ChenBGI TECHTel: +86-131-2890-7008 QQ: 751962963 Email: che...@ge... Building 10F│Beishan Industrial Zone│Yantian District│Shenzhen 518083│China 
 From: che...@ge...: 2015-04-01 18:50To: mum...@li...: Re: confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6
confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6I cut qury files and then run nucmer agianst genome. then I cat the result of nucmer(*.delta), and run dealta-filter on cat files. However, it warned: /opt/blc/genome/biosoft/MUMmer-3.22/delta-filter   -q  test0ERROR: Could not parse delta file, test0

error no: 400
I do not know whywould you like to  give us some help?many thaks.best regards for you. 



----------------Junhui ChenBGI TECHTel: +86-131-2890-7008 QQ: 751962963 Email: che...@ge... Building 10F│Beishan Industrial Zone│Yantian District│Shenzhen 518083│China 
 From: mum...@li...: 2015-04-01 18:45To: che...@ge...: confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6Mailing list subscription confirmation notice for mailing list
MUMmer-help
 
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[MUMmer-help] Fw: Re: confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6

[<che...@ge...>]

----------------Junhui ChenBGI TECHTel: +86-131-2890-7008 QQ: 751962963 Email: che...@ge... Building 10F│Beishan Industrial Zone│Yantian District│Shenzhen 518083│China 
 From: che...@ge...: 2015-04-01 18:50To: mum...@li...: Re: confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6
confirm 8dd1127d8ff2e4050d0eea18a0ba9c28c93db7e6I cut qury files and then run nucmer agianst genome. then I cat the result of nucmer(*.delta), and run dealta-filter on cat files. However, it warned: /opt/blc/genome/biosoft/MUMmer-3.22/delta-filter   -q  test0ERROR: Could not parse delta file, test0

error no: 400
I do not know whywould you like to  give us some help?many thaks.best regards for you. 



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Re: [MUMmer-help] whole genome alignment question

[Diogo C. <dio...@gm...>]

That’s what I thought.  I aligned my reference to a very similar (same genus, same species, different strain bacterium) and I got a very high similarity and a very high percentage of aligned bases.  Thanks for the tip on nucmer.  I’ll explore that some more to fit my needs.


----------
Diogo Camacho
e: dio...@gm...
p: (617) 945-4383





> On Mar 3, 2015, at 11:48 AM, Adam Phillippy <aph...@gm...> wrote:
> 
> You are reading that correctly. With default options, Nucmer's sensitivity is tuned for alignments >90% identity. Your genomes are likely too divergent to align well w/ these parameters. If they are small bacterial genomes you could try something like:
> 
> nucmer -maxmatch -l 18 -c 50 -g 200
> 
> To improve sensitivity, but in general the tool is not well suited for sensitive alignments.
> 
> -Adam
> 
> 
> On Tue, Mar 3, 2015 at 11:31 AM, Diogo Camacho <dio...@gm...> wrote:
> A follow up to my earlier question:  when I looked at the output from dnadiff (the .report file) I saw this:
> 
> [Bases]
> TotalBases                   1837281              2427048
> AlignedBases            47871(2.61%)         47261(1.95%)
> UnalignedBases       1789410(97.39%)      2379787(98.05%)
> 
> [Alignments]
> 1-to-1                            28                   28
> TotalLength                    23369                23403
> AvgLength                     834.61               835.82
> AvgIdentity                    83.96                83.96
> 
> M-to-M                            67                   67
> TotalLength                    86329                86650
> AvgLength                    1288.49              1293.28
> AvgIdentity                    87.96                87.96
> 
> 
> Does this output mean that I’m only really aligning the query genome to roughly 3% of my reference genome, and that alignment has an average identity of 80%+?   Or am I reading this wrong?
> 
> Thanks!
> 
> 
> 
> ----------
> Diogo Camacho
> e: dio...@gm...
> p: (617) 945-4383
> 
> 
> 
> 
> 
> > On Mar 3, 2015, at 10:30 AM, Adam Phillippy <aph...@gm...> wrote:
> >
> > Hi Diogo,
> > If you run the 'dnadiff' script that comes with MUMmer it will generate a .report file that will include global similarity metrics based on Nucmer alignments.
> >
> > Best,
> > -Adam
> >
> >
> > On Tue, Mar 3, 2015 at 9:50 AM, Diogo Camacho <dio...@gm...> wrote:
> > Hi,
> >
> > This is a very naive, simple question, but I can’t seem to locate a good answer for it on the manual.  I have a set of bacterial genomes that I want to align against a different (single) bacterial genome.  The obvious tool to do this seems to be NUCmer and I did a test run of 1 genome against the “reference” genome by doing:
> >
> > nucmer -maxmatch -p test-output <REFERENCE GENOME> <GENOME TO BE COMPARED>
> >
> > NUCmer runs fine and when I do show-coords I get the table with the alignments and the respective identity between the 2 genomes I am comparing.  But what I would like would be to get a single, global, percent identity score between the 2 genomes, as I basically want to compare the two genomes at a global level.  Is there a simple way to do this using the MUMer suite?
> >
> > Many thanks!
> >
> >
> > Best,
> > d.
> >
> >
> >
> > ----------
> > Diogo Camacho
> > e: dio...@gm...
> > p: (617) 945-4383
> >
> >
> >
> >
> >
> >
> > ------------------------------------------------------------------------------
> > Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> > by Intel and developed in partnership with Slashdot Media, is your hub for all
> > things parallel software development, from weekly thought leadership blogs to
> > news, videos, case studies, tutorials and more. Take a look and join the
> > conversation now. http://goparallel.sourceforge.net/
> > _______________________________________________
> > MUMmer-help mailing list
> > MUM...@li...
> > https://lists.sourceforge.net/lists/listinfo/mummer-help
> >
> 
> 

Re: [MUMmer-help] whole genome alignment question

[Adam P. <aph...@gm...>]

You are reading that correctly. With default options, Nucmer's sensitivity
is tuned for alignments >90% identity. Your genomes are likely too
divergent to align well w/ these parameters. If they are small bacterial
genomes you could try something like:

nucmer -maxmatch -l 18 -c 50 -g 200

To improve sensitivity, but in general the tool is not well suited for
sensitive alignments.

-Adam


On Tue, Mar 3, 2015 at 11:31 AM, Diogo Camacho <dio...@gm...
> wrote:

> A follow up to my earlier question:  when I looked at the output from
> dnadiff (the .report file) I saw this:
>
> [Bases]
> TotalBases                   1837281              2427048
> AlignedBases            47871(2.61%)         47261(1.95%)
> UnalignedBases       1789410(97.39%)      2379787(98.05%)
>
> [Alignments]
> 1-to-1                            28                   28
> TotalLength                    23369                23403
> AvgLength                     834.61               835.82
> AvgIdentity                    83.96                83.96
>
> M-to-M                            67                   67
> TotalLength                    86329                86650
> AvgLength                    1288.49              1293.28
> AvgIdentity                    87.96                87.96
>
>
> Does this output mean that I’m only really aligning the query genome to
> roughly 3% of my reference genome, and that alignment has an average
> identity of 80%+?   Or am I reading this wrong?
>
> Thanks!
>
>
>
> ----------
> Diogo Camacho
> e: dio...@gm...
> p: (617) 945-4383
>
>
>
>
>
> > On Mar 3, 2015, at 10:30 AM, Adam Phillippy <aph...@gm...>
> wrote:
> >
> > Hi Diogo,
> > If you run the 'dnadiff' script that comes with MUMmer it will generate
> a .report file that will include global similarity metrics based on Nucmer
> alignments.
> >
> > Best,
> > -Adam
> >
> >
> > On Tue, Mar 3, 2015 at 9:50 AM, Diogo Camacho <
> dio...@gm...> wrote:
> > Hi,
> >
> > This is a very naive, simple question, but I can’t seem to locate a good
> answer for it on the manual.  I have a set of bacterial genomes that I want
> to align against a different (single) bacterial genome.  The obvious tool
> to do this seems to be NUCmer and I did a test run of 1 genome against the
> “reference” genome by doing:
> >
> > nucmer -maxmatch -p test-output <REFERENCE GENOME> <GENOME TO BE
> COMPARED>
> >
> > NUCmer runs fine and when I do show-coords I get the table with the
> alignments and the respective identity between the 2 genomes I am
> comparing.  But what I would like would be to get a single, global, percent
> identity score between the 2 genomes, as I basically want to compare the
> two genomes at a global level.  Is there a simple way to do this using the
> MUMer suite?
> >
> > Many thanks!
> >
> >
> > Best,
> > d.
> >
> >
> >
> > ----------
> > Diogo Camacho
> > e: dio...@gm...
> > p: (617) 945-4383
> >
> >
> >
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> > by Intel and developed in partnership with Slashdot Media, is your hub
> for all
> > things parallel software development, from weekly thought leadership
> blogs to
> > news, videos, case studies, tutorials and more. Take a look and join the
> > conversation now. http://goparallel.sourceforge.net/
> > _______________________________________________
> > MUMmer-help mailing list
> > MUM...@li...
> > https://lists.sourceforge.net/lists/listinfo/mummer-help
> >
>
>

Re: [MUMmer-help] whole genome alignment question

[Diogo C. <dio...@gm...>]

A follow up to my earlier question:  when I looked at the output from dnadiff (the .report file) I saw this:

[Bases]
TotalBases                   1837281              2427048
AlignedBases            47871(2.61%)         47261(1.95%)
UnalignedBases       1789410(97.39%)      2379787(98.05%)

[Alignments]
1-to-1                            28                   28
TotalLength                    23369                23403
AvgLength                     834.61               835.82
AvgIdentity                    83.96                83.96

M-to-M                            67                   67
TotalLength                    86329                86650
AvgLength                    1288.49              1293.28
AvgIdentity                    87.96                87.96


Does this output mean that I’m only really aligning the query genome to roughly 3% of my reference genome, and that alignment has an average identity of 80%+?   Or am I reading this wrong? 

Thanks!



----------
Diogo Camacho
e: dio...@gm...
p: (617) 945-4383





> On Mar 3, 2015, at 10:30 AM, Adam Phillippy <aph...@gm...> wrote:
> 
> Hi Diogo,
> If you run the 'dnadiff' script that comes with MUMmer it will generate a .report file that will include global similarity metrics based on Nucmer alignments.
> 
> Best,
> -Adam
> 
> 
> On Tue, Mar 3, 2015 at 9:50 AM, Diogo Camacho <dio...@gm...> wrote:
> Hi,
> 
> This is a very naive, simple question, but I can’t seem to locate a good answer for it on the manual.  I have a set of bacterial genomes that I want to align against a different (single) bacterial genome.  The obvious tool to do this seems to be NUCmer and I did a test run of 1 genome against the “reference” genome by doing:
> 
> nucmer -maxmatch -p test-output <REFERENCE GENOME> <GENOME TO BE COMPARED>
> 
> NUCmer runs fine and when I do show-coords I get the table with the alignments and the respective identity between the 2 genomes I am comparing.  But what I would like would be to get a single, global, percent identity score between the 2 genomes, as I basically want to compare the two genomes at a global level.  Is there a simple way to do this using the MUMer suite?
> 
> Many thanks!
> 
> 
> Best,
> d.
> 
> 
> 
> ----------
> Diogo Camacho
> e: dio...@gm...
> p: (617) 945-4383
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
> 

Re: [MUMmer-help] whole genome alignment question

[Diogo C. <dio...@gm...>]

Hi Adam,

Thanks for the tip.  Just tried it out and looking at the .report file I can see the average identity between the 2 genomes.  Thanks!


Best,
d.



----------
Diogo Camacho
e: dio...@gm...
p: (617) 945-4383





> On Mar 3, 2015, at 10:30 AM, Adam Phillippy <aph...@gm...> wrote:
> 
> Hi Diogo,
> If you run the 'dnadiff' script that comes with MUMmer it will generate a .report file that will include global similarity metrics based on Nucmer alignments.
> 
> Best,
> -Adam
> 
> 
> On Tue, Mar 3, 2015 at 9:50 AM, Diogo Camacho <dio...@gm...> wrote:
> Hi,
> 
> This is a very naive, simple question, but I can’t seem to locate a good answer for it on the manual.  I have a set of bacterial genomes that I want to align against a different (single) bacterial genome.  The obvious tool to do this seems to be NUCmer and I did a test run of 1 genome against the “reference” genome by doing:
> 
> nucmer -maxmatch -p test-output <REFERENCE GENOME> <GENOME TO BE COMPARED>
> 
> NUCmer runs fine and when I do show-coords I get the table with the alignments and the respective identity between the 2 genomes I am comparing.  But what I would like would be to get a single, global, percent identity score between the 2 genomes, as I basically want to compare the two genomes at a global level.  Is there a simple way to do this using the MUMer suite?
> 
> Many thanks!
> 
> 
> Best,
> d.
> 
> 
> 
> ----------
> Diogo Camacho
> e: dio...@gm...
> p: (617) 945-4383
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
> 

Re: [MUMmer-help] whole genome alignment question

[Adam P. <aph...@gm...>]

Hi Diogo,
If you run the 'dnadiff' script that comes with MUMmer it will generate a
.report file that will include global similarity metrics based on Nucmer
alignments.

Best,
-Adam


On Tue, Mar 3, 2015 at 9:50 AM, Diogo Camacho <dio...@gm...>
wrote:

> Hi,
>
> This is a very naive, simple question, but I can’t seem to locate a good
> answer for it on the manual.  I have a set of bacterial genomes that I want
> to align against a different (single) bacterial genome.  The obvious tool
> to do this seems to be NUCmer and I did a test run of 1 genome against the
> “reference” genome by doing:
>
> nucmer -maxmatch -p test-output <REFERENCE GENOME> <GENOME TO BE COMPARED>
>
> NUCmer runs fine and when I do show-coords I get the table with the
> alignments and the respective identity between the 2 genomes I am
> comparing.  But what I would like would be to get a single, global, percent
> identity score between the 2 genomes, as I basically want to compare the
> two genomes at a global level.  Is there a simple way to do this using the
> MUMer suite?
>
> Many thanks!
>
>
> Best,
> d.
>
>
>
> ----------
> Diogo Camacho
> e: dio...@gm...
> p: (617) 945-4383
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for
> all
> things parallel software development, from weekly thought leadership blogs
> to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> MUMmer-help mailing list
> MUM...@li...
> https://lists.sourceforge.net/lists/listinfo/mummer-help
>

[MUMmer-help] whole genome alignment question

[Diogo C. <dio...@gm...>]

Hi,

This is a very naive, simple question, but I can’t seem to locate a good answer for it on the manual.  I have a set of bacterial genomes that I want to align against a different (single) bacterial genome.  The obvious tool to do this seems to be NUCmer and I did a test run of 1 genome against the “reference” genome by doing:

nucmer -maxmatch -p test-output <REFERENCE GENOME> <GENOME TO BE COMPARED>

NUCmer runs fine and when I do show-coords I get the table with the alignments and the respective identity between the 2 genomes I am comparing.  But what I would like would be to get a single, global, percent identity score between the 2 genomes, as I basically want to compare the two genomes at a global level.  Is there a simple way to do this using the MUMer suite?  

Many thanks!


Best,
d.



----------
Diogo Camacho
e: dio...@gm...
p: (617) 945-4383

Re: [MUMmer-help] nucmer error

[Adam P. <aph...@gm...>]

Hi Chris,
Have seen this error on the MUMmer list before. Here was the solution:

"Figured this one out - had a bracket in my folder name!"

Likely some sort of filename / environment issue.

-Adam


On Mon, Feb 23, 2015 at 7:17 AM, Wymant, Chris <c.w...@im...>
wrote:

>  Dear MUMmer help,
>
> >From a clean install of MUMmer, running
> $ nucmer --maxmatch test1.fa test2.fa
> gives the output
> 1: PREPARING DATA
> sh: 1: Syntax error: "(" unexpected
> ERROR: prenuc returned non-zero
> regardless of what is in the fasta files; for example just
> >MySequence
> ACTG
> still gives the error. Changing the --maxmatch option does not help.
> Please advise.
>
> Thanks,
> Chris Wymant
>
>
> ------------------------------------------------------------------------------
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