inchworm-users Mailing List for inchworm (Page 2)
Brought to you by:
bhaas
You can subscribe to this list here.
2010 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
(2) |
Oct
(4) |
Nov
(2) |
Dec
|
---|---|---|---|---|---|---|---|---|---|---|---|---|
2011 |
Jan
|
Feb
(11) |
Mar
(5) |
Apr
|
May
(2) |
Jun
|
Jul
|
Aug
|
Sep
(2) |
Oct
(3) |
Nov
|
Dec
|
From: Brian H. <bh...@br...> - 2010-10-08 18:01:34
|
Greetings all. A new version of inchworm is now available at sourceforge. It includes a critical bugfix to restore a functional --DS (double stranded) mode, which seg-faulted in the previous version. Thanks to Don Gilbert for reporting the error and identifying the problem. Note, for improved memory usage, you can leverage the 'google sparse hash'. Instructions are provided in the README file. Best regards, -Brian -- -- Brian J. Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas |
From: Brian H. <bh...@br...> - 2010-10-07 20:18:08
|
Hi Don, Give inchworm a try. Inchworm is integrated into the latest version of PASA, too, so you could give that a whirl. Compared to other de novo assemblers, Inchworm should generate more 'full-length' transcript contigs, and so provides a more complete resources for de-novo assembly without a genome, and with its tie-in to PASA, provides a useful genome annotation tool. I'm curious how inchworm (or more specifically, inchworm & PASA) fare in your comparisons. Since you have EST and cDNA data, along with RNA-Seq, I'd suggest running PASA in RNA-Seq mode first. Then, taking the resulting PASA assemblies, combining them with your ESTs and cDNAs, and run them through PASA again a second time in 'regular' PASA mode (not using the --RNASeq option). I suggest doing these as separate rounds because PASA treats the inchworm assemblies in a special way (first round), removing noise and artifacts that result from deep sequencing. Also, when you run the pasa-assemblies of Inchworm through PASA in that second round, be sure to mangle the accession somehow.... PASA looks for sequences called 'asmbl...' and treats them differently. Keep in touch, -Brian On Thu, Oct 7, 2010 at 1:29 PM, don gilbert <gil...@in...> wrote: > Brian, > > Thanks for providing this new software for RNA-seq assembly. I'm > looking now for a de-novo assembler, which this seems to be, but have > other choices like Velvet, Oasis, ... What makes Inchworm better, or > competitive with these other choices? > > I've been using RNA-seq data combined with other gene evidence for > making better gene models, with reasonable success. I map the reads > to genome with GSNAP then use Cufflinks to assemble. Then I mix these > with ESTs using PASA for more complete assemblies. This seems to work (http://arthropods.eugenes.org/genes2/ > ). > > However I recently compared de-novo assemblies provided by NCBI's TSA, > with genome-mapped/assembled assemblies of the same RNA-seq data (for > pea aphid). To my surprise there is only 50% agreement. The de-novo > assemblies, mapped to genome with GMAP, cover a bit more of the genome. > > But also both assemblies appear to include a large chunk valid read > expression the other doesn't, measured against protein homology and > longer ESTs. Perhaps this shouldn't be a surprise, as the problems of > read assembly with or without genome mapping are somewhat different. > > - Don Gilbert > > > -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 > -- gil...@in... -- http://marmot.bio.indiana.edu/ > > > ------------------------------------------------------------------------------ > Beautiful is writing same markup. Internet Explorer 9 supports > standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. > Spend less time writing and rewriting code and more time creating great > experiences on the web. Be a part of the beta today. > http://p.sf.net/sfu/beautyoftheweb > _______________________________________________ > Inchworm-users mailing list > Inc...@li... > https://lists.sourceforge.net/lists/listinfo/inchworm-users > -- -- Brian J. Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas |
From: don g. <gil...@in...> - 2010-10-07 17:47:32
|
Brian, Thanks for providing this new software for RNA-seq assembly. I'm looking now for a de-novo assembler, which this seems to be, but have other choices like Velvet, Oasis, ... What makes Inchworm better, or competitive with these other choices? I've been using RNA-seq data combined with other gene evidence for making better gene models, with reasonable success. I map the reads to genome with GSNAP then use Cufflinks to assemble. Then I mix these with ESTs using PASA for more complete assemblies. This seems to work (http://arthropods.eugenes.org/genes2/ ). However I recently compared de-novo assemblies provided by NCBI's TSA, with genome-mapped/assembled assemblies of the same RNA-seq data (for pea aphid). To my surprise there is only 50% agreement. The de-novo assemblies, mapped to genome with GMAP, cover a bit more of the genome. But also both assemblies appear to include a large chunk valid read expression the other doesn't, measured against protein homology and longer ESTs. Perhaps this shouldn't be a surprise, as the problems of read assembly with or without genome mapping are somewhat different. - Don Gilbert -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405 -- gil...@in... -- http://marmot.bio.indiana.edu/ |
From: Brian H. <bh...@br...> - 2010-10-01 14:25:16
|
Greetings all. A new version of Inchworm is available on sourceforge: http://inchworm.sf.net It includes: -improved installation procedure, using configure/make/make-install -no longer requires BOOST libraries and is now fully independent of 3rd party software, easing installation. -menu is simpler and less cluttered. Advanced options are shown with the --show_advanced parameter. -iwormVaryK.pl is included, allowing one to iterate through values of Kmer lengths and combining the results seamlessly. -improved memory handling (about half as much memory required as the earlier version, on average). -fewer artifacts reported (contigs with average kmer coverage >= 2 are reported; parameter can be changed). -documentation on sourceforge site is updated and improved. -test data is included in the distribution for both inchworm and iwormVaryK Enjoy! -brian -- -- Brian J. Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas |
From: Brian H. <bh...@br...> - 2010-09-24 13:31:01
|
Hi Axel, Inchworm can work well with non-strand-specific RNA-Seq, but it definitely does better with strand-specific data. Just be sure to run it with the --DS parameter. If you're doing this in a completely de novo sense and have no genome to compare to, you might consider using CD-HIT to remove artifacts that map to better quality contigs. Best regards, -Brian Non-strand specificFri Sep 24 2010 05:56:28 GMT-0400 (EDT) From: "Axel Künstner" <Axe...@eb...> To: "" <inc...@li...> Hey, I was wondering whether you just recommend strand specific data or whether it is necessary to use it to get meaningful assemblies from inchworm. I`m working with RNA-seq data from non-model organisms and I`m testing several de-novo assembly strategies at the moment. Thanks for your help, Axel -- -- Brian J. Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas |
From: Axel K. <Axe...@eb...> - 2010-09-24 10:16:01
|
Hey, I was wondering whether you just recommend strand specific data or whether it is necessary to use it to get meaningful assemblies from inchworm. I`m working with RNA-seq data from non-model organisms and I`m testing several de-novo assembly strategies at the moment. Thanks for your help, Axel -- Axel Künstner PhD student Department of Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Norbyvägen 18D SE-752 36 Uppsala Sweden Phone: +46 18 471 6468 email: axe...@eb... |