Comments on: NextGen Aligner Focus Group

By: Roald Forsberg

Roald Forsberg — Tue, 12 Aug 2008 08:12:21 +0000

We believe that we have a very strong assembler for short reads.
You can get the white paper of our website http://www.clcbio.com

By: zee

zee — Wed, 06 Aug 2008 05:38:56 +0000

In case anybody’s interested in trying novocraft, the aligners (novopaired + novoalign) is free for use an can be downloaded at http://www.novocraft.com

By: MB

MB — Mon, 04 Aug 2008 09:18:15 +0000

Fairly a good list! In addition, it seems to me that ZOOM (http://www.bioinformaticssolutions.com/products/ph/ZOOM.pdf) is another worthy candidate. It is developed by the group of people who wrote PatternHunter. In my view, it is a strong group.

ZOOM will be acadmic free and is going to be released in a few weeks, according to an email sent by that group.

By: benbfly

benbfly — Sat, 19 Jul 2008 21:43:42 +0000

I’ve also heard Shrimp (http://compbio.cs.toronto.edu/shrimp/) gives good results (I am not affiliated and have not even tried it yet). I know people who are using RMAP, so i think it’s worth including.

By: jhui

jhui — Tue, 24 Jun 2008 21:29:41 +0000

if possible, please include SeqMap(http://biogibbs.stanford.edu/~jiangh/SeqMap/) into the list. It works like ELand, but can do 3 or more mismatches and also ins/del.

By: admin

admin — Tue, 24 Jun 2008 21:15:42 +0000

My friends at GTO picked up this entry in their Daily Scan: http://www.genome-technology.com/issues/blog/general/147733-1.html

They noted that the aligners we’re testing “include Maq, Eland, BLAT, and cross_match.” In fairness, we’re also looking at a few others in the first evaluation. Here’s the list of prioritized aligners by sequencing platform:

Illumina/Solexa Data
-Maq
-Eland
-New CrossMatch
-SlimSearch
-Novocraft
-Mosaik

Roche/454 Data
-BLAT
-New CM
-Mosaik
-GsMapper
-SynaSearch