SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to build reference genome for targeted region(from a BED file) for alignment? serenaliao Epigenetics 6 08-07-2015 01:44 PM
bowtie2 gapped alignment Bulak Bioinformatics 0 03-11-2013 07:39 AM
alignment speed on workstation vs desktop a_mt Bioinformatics 4 01-18-2013 11:43 PM
bowtie2 stops during alignment moritzhess Bioinformatics 3 01-13-2013 03:53 AM
c.elegans genome alignment recommended settings for BFAST hylei Bioinformatics 0 03-18-2011 07:36 AM

Reply
 
Thread Tools
Old 08-29-2013, 12:28 PM   #1
biznatch
Senior Member
 
Location: Canada

Join Date: Nov 2010
Posts: 124
Default Bowtie2-build settings to speed up alignment

The bowtie2-build indexer lists several performance options. I am unsure about what some of these do, and about whether they can be used to increase the performance (speed up) just the index building or if they will help make the actual aligning process faster. Bowtie uses less than 5 GB of memory while aligning, I am happy to let Bowtie use more memory (up to about 16 GB) if it will make the alignment process faster.

bmax/bmaxdivn: These two are related to each other. For bmax is it says, "Default (in terms of the --bmaxdivn parameter) is --bmaxdivn 4." So the default is to set bmaxdivn to 4, and if I set bmaxdivn lower it will use more memory but make the alignment faster?

dcv: "A larger period yields less memory overhead, but may make suffix sorting slower, ... Default: 1024." So if I set this to 256 will it make my alignment faster?

offrate: "the indexer will mark every 2^<int> rows. Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime. The default is 5 (every 32nd row is marked;". I could set this to 1 or 2 to get a faster alignment?

ftabchars: "A larger <int> yields a larger lookup table but faster query times. The ftab has size 4^(<int>+1) bytes. The default setting is 10". I could try 12 or 14 to get a faster alignment?
biznatch is offline   Reply With Quote
Reply

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 09:07 AM.


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