Re: [wgs-assembler-users] Question about contaminant trimming and referring quality value

[Takashi K. <tak...@gm...>]

I will test both. Thanks guys!!

2015-03-14 12:07 GMT+09:00 Liu, Xinyue <xy...@so...>:

>  To run Consed while bypassing phd files you can run "consed -nophd". But
> as Brian pointed out it might crash with big assemblies. Another assembly
> viewer I used to run on CA assemblies is Hawkeye (
> http://amos.sourceforge.net/wiki/index.php?title=Hawkeye).
>
>  Best,
> Jerry
>
>  ------------------------------
> *From:* Brian Walenz [th...@gm...]
> *Sent:* Friday, March 13, 2015 10:13 PM
> *To:* Takashi Koyama
> *Cc:* wgs...@li...
> *Subject:* Re: [wgs-assembler-users] Question about contaminant trimming
> and referring quality value
>
>    I'll be no help on visualization.  Most of the things I've assembled
> were too big for that.
>
>  For trimming, the assembler will do a respectable job without cleaning up
> vector.  Reads with both vector and genomic sequence will look like
> chimera, and will have the smaller portion removed.  Reads of entire vector
> will assemble together, and will need to be screened from the output.  Mate
> pairs across the junction (one read vector, one read genomic) are a
> potential problem, and could confuse the scaffold graph enough to prevent
> assembly.
>
> If you have high coverage Illumina, mapping to the ecoli/vector and
> discarding the entire pair for any hit is the simplest and safest.  Bowtie2
> will do this, but I forget the option.
>
> It's been a long time since I've had to clean up Sanger reads, and
> hopefully I can continue forgetting how to do it.
>
>  In all cases, your best bet is to hard trim -- remove the vector/ecoli
> sequence from the reads -- before giving the reads to the assembler.  Don't
> pass in a clear range to the assembler, as it will probably ignore it.
>
>  b
>
>
> On Fri, Mar 13, 2015 at 9:18 AM, Takashi Koyama <tak...@gm...>
> wrote:
>
>>    Hello, I have two questions.
>>
>>  First question. I now trying to assemble BAC clones. As BAC samples
>> include BAC vector and some of E. coli genome, assemblers I've ever used
>> refer vector and E. coli fasta sequences to trim them. However, I could not
>> find an instruction to do that in celera assembly.
>>  Is it possible to refer some fasta files for trimming in CA? Or if
>> impossible, could anyone tell me how I trim them in CA?
>>
>>  Second question. I would like to see how good CA works by assembly
>> viewer. I usually use Consed. I could get an ace file using ca2ace.pl
>> and open it in Consed. However, Consed told me there is no quality files
>> such as phd file. Could anyone tell me any solutions making Consed work
>> smooth?
>>
>>  Thank you for your kind helps.
>>
>>  TK
>>
>>
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>