Comments on: Short Read Aligners Update at AGBT http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html Medical genomics in the post-genome era Fri, 27 Apr 2012 18:07:26 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: admin http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-148 admin Mon, 02 Feb 2009 14:17:11 +0000 http://www.massgenomics.org/?p=126#comment-148 You make a good point, MB - there are certainly commercial options for short read alignment out there. Trouble is, when freely available and open source tools like Maq are comparable to a commercial product, what's the motivation for anyone to spend ever-more-limited funding on the latter? Nevertheless, I was offered a trial license to CLCbio's CELL2 and hope to include the program in my poster. You make a good point, MB – there are certainly commercial options for short read alignment out there. Trouble is, when freely available and open source tools like Maq are comparable to a commercial product, what’s the motivation for anyone to spend ever-more-limited funding on the latter? Nevertheless, I was offered a trial license to CLCbio’s CELL2 and hope to include the program in my poster.

]]> By: MB http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-144 MB Sat, 24 Jan 2009 20:42:27 +0000 http://www.massgenomics.org/?p=126#comment-144 I know you only use freeware in your work. Me, too. However, it is still worth trying non-free programs such as ZOOM and CLC Bio. There are reasons why they dare to ask for thousands of dollars in this competitive area. My experience is ZOOM is really an attractive software. It seems to me that ZOOM achieves a good balance between effeciency and accuracy. Soap2 is fast, but it allows at most two mismatches at the moment; novoalign is accurate, but it is a little bit slow. I know you only use freeware in your work. Me, too. However, it is still worth trying non-free programs such as ZOOM and CLC Bio. There are reasons why they dare to ask for thousands of dollars in this competitive area. My experience is ZOOM is really an attractive software. It seems to me that ZOOM achieves a good balance between effeciency and accuracy. Soap2 is fast, but it allows at most two mismatches at the moment; novoalign is accurate, but it is a little bit slow.

]]> By: Zee http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-143 Zee Fri, 23 Jan 2009 02:46:44 +0000 http://www.massgenomics.org/?p=126#comment-143 In All fairness to the BWA developer I need to mention that I downloaded BWA 0.4.1 this week and gave it another try and it worked beautifully. In All fairness to the BWA developer I need to mention that I downloaded BWA 0.4.1 this week and gave it another try and it worked beautifully.

]]> By: Matt http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-142 Matt Thu, 22 Jan 2009 22:28:00 +0000 http://www.massgenomics.org/?p=126#comment-142 Have you looked at MIRA, and if so, any impressions? Have you looked at MIRA, and if so, any impressions?

]]> By: PolITiGenomics » Blog Archive » Next-Generation Informatics at AGBT http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-141 PolITiGenomics » Blog Archive » Next-Generation Informatics at AGBT Thu, 22 Jan 2009 18:23:28 +0000 http://www.massgenomics.org/?p=126#comment-141 [...] Several other people from The Genome Center will also be attending and presenting. Our Director, Rick Wilson, will be giving a keynote address on Saturday. Co-Director Elaine Mardis will chair the always interesting New Genomic Frontiers plenary session (don’t make the mistake of booking that early flight, you’ll miss the best stuff). Todd Wylie and Jon Armstrong from our Technology Development group will be giving talks on miRNA characterization and capture techniques, respectively. Also, be sure to check out Dan Koboldt’s blog post giving a sneak preview of the poster he will be presenting about the performance of various short-read aligners. [...] [...] Several other people from The Genome Center will also be attending and presenting. Our Director, Rick Wilson, will be giving a keynote address on Saturday. Co-Director Elaine Mardis will chair the always interesting New Genomic Frontiers plenary session (don’t make the mistake of booking that early flight, you’ll miss the best stuff). Todd Wylie and Jon Armstrong from our Technology Development group will be giving talks on miRNA characterization and capture techniques, respectively. Also, be sure to check out Dan Koboldt’s blog post giving a sneak preview of the poster he will be presenting about the performance of various short-read aligners. [...]

]]> By: admin http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-140 admin Thu, 22 Jan 2009 16:23:17 +0000 http://www.massgenomics.org/?p=126#comment-140 Thanks for the comments, everyone. Yes, I'll undoubtedly post my results (and hopefully my entire poster) after AGBT. AS, you can reach me at dkoboldt [at] genetics [dot] wustl [dot] edu. Thanks for the comments, everyone. Yes, I’ll undoubtedly post my results (and hopefully my entire poster) after AGBT.

AS, you can reach me at dkoboldt [at] genetics [dot] wustl [dot] edu.

]]> By: Nicolas Delhomme http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-139 Nicolas Delhomme Thu, 22 Jan 2009 10:19:28 +0000 http://www.massgenomics.org/?p=126#comment-139 Sounds good! Sadly I won't be attending AGBT this year. Will you make your poster and data available after the conference? Sounds good! Sadly I won’t be attending AGBT this year. Will you make your poster and data available after the conference?

]]> By: AS http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-138 AS Thu, 22 Jan 2009 03:26:53 +0000 http://www.massgenomics.org/?p=126#comment-138 Hi Dan, I have some interesting ideas about use of MAQ. Can you please share your contact information? I would like to run my ideas by you and get your thoughts. Thanks. Hi Dan,

I have some interesting ideas about use of MAQ. Can you please share your contact information? I would like to run my ideas by you and get your thoughts.

Thanks.

]]> By: sm http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-137 sm Wed, 21 Jan 2009 20:42:02 +0000 http://www.massgenomics.org/?p=126#comment-137 Are you able to comment/share experience with MAQ on paired-end data, especially on its sv script for structural variants. What is the confidence in structural variants and indels detected by MAQ paired end module? Are you able to comment/share experience with MAQ on paired-end data, especially on its sv script for structural variants.
What is the confidence in structural variants and indels detected by MAQ paired end module?

]]> By: Ben Langmead http://massgenomics.org/2009/01/short-read-aligners-update-at-agbt.html/comment-page-1#comment-135 Ben Langmead Wed, 21 Jan 2009 18:58:22 +0000 http://www.massgenomics.org/?p=126#comment-135 Hello Dan, I am the main author of Bowtie and I wanted to note that a version of Bowtie with initial paired-end functionality should be available in a few weeks. That's currently my highest priority. I'm trying to get it done before AGBT, where I'll present a poster on Bowtie. Thanks! - great blog, Ben Hello Dan,
I am the main author of Bowtie and I wanted to note that a version of Bowtie with initial paired-end functionality should be available in a few weeks. That’s currently my highest priority. I’m trying to get it done before AGBT, where I’ll present a poster on Bowtie.
Thanks! – great blog,
Ben

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