Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Aligning numerous reads to several small references R diggity Bioinformatics 3 07-10-2010 12:26 PM
Tophat/Cufflinks/RNASeq short-read aligners and pseudogenes sjm RNA Sequencing 2 01-20-2010 05:09 AM
Running MAQ SNP/Indel detection/Assembly Tools on short aligners zee Bioinformatics 4 12-11-2009 01:41 PM
The Short Read Headache doxologist Literature Watch 0 02-13-2009 10:01 AM
short reads missed by aligners bioinfosm Bioinformatics 10 08-08-2008 02:50 AM

Thread Tools
Old 04-20-2011, 03:15 PM   #1
Senior Member
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
Default Numerous short read aligners: But which is best?

Hi All,

There seems to be a bunch of competing packages out there (MIRA3, Abyss, Velvet, Bowtie etc), but I wonder if anyone can offer a comparative synopsis of the data produced by each?

Has anyone compared assemblies between these packages, and which did they find most robust/reliable/erroneous/automated etc/?

My interests at the moment surround transcripome assemblies, and have been using MIRA3 and Geneious (which i think uses Bowtie). The incorporation of QUAL files in MIRA3 assemblies seems like a good idea.
Any thoughts?


JackieBadger is offline   Reply With Quote
Old 04-20-2011, 06:17 PM   #2
Nils Homer
nilshomer's Avatar
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

nilshomer is offline   Reply With Quote
Old 04-20-2011, 09:19 PM   #3
Curious Character
Location: Berlin, Germany

Join Date: Sep 2010
Posts: 13

Evaluation of asssembly algorithms

BTW, MIRA3 is de novo assembly, while Bowtie is short read aligner. Not sure, but I think Geneious use their own algorithm.
kokonech is offline   Reply With Quote
Old 04-21-2011, 02:17 AM   #4
Senior Member
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381

cheers, guys

JackieBadger is offline   Reply With Quote
Old 04-28-2011, 11:02 AM   #5
Registered Vendor
Location: New Zealand

Join Date: Jul 2010
Posts: 22

Hi, Yes, Geneious uses its own algorithm inside Geneious Pro, however Geneious Server allows users on the desktops to run a range of different mappers and assemblers including SOAP2, BWA, MAQ, Bowtie and Velvet in addition to the Geneious Reference Assembler and the Geneious de novo Assembler
Geneious is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:14 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO