SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to extract multi-mapped reads by samtools? mavishou RNA Sequencing 5 12-05-2016 06:27 AM
Compile multi-individual SNP tables from bowtie/samtools mappings KNS Bioinformatics 10 12-02-2011 09:40 AM
RTG Investigator 2.3: New Ion Torrent support, faster Complete Genomics mapping Stuart Inglis Vendor Forum 0 08-31-2011 02:27 PM
samtools flagstats bug or it does not support multi-reads? xinwu Bioinformatics 0 12-22-2010 10:33 PM
Cuffdiff multi-protein vs multi-promoter RockChalkJayhawk Bioinformatics 2 03-26-2010 11:26 AM

Reply
 
Thread Tools
Old 05-14-2013, 01:35 PM   #61
narain
Member
 
Location: Washington DC

Join Date: Aug 2011
Posts: 78
Default

So what is the update with this project https://github.com/nh13/samtools . Is it still faster than multi-threaded version of samtools ? Is this going to be a good substitute for Goby and Cram ?
narain is offline   Reply With Quote
Old 05-14-2013, 01:38 PM   #62
narain
Member
 
Location: Washington DC

Join Date: Aug 2011
Posts: 78
Default

Has there been any success on mpileup speedup ? Is the parallelization by pthreads or MPI ?
narain is offline   Reply With Quote
Old 06-11-2013, 07:04 PM   #63
abi
Member
 
Location: Blacksburg

Join Date: May 2013
Posts: 18
Default

Is the bcftools that come with samtools also multithreaded ?
abi is offline   Reply With Quote
Old 06-29-2013, 08:32 PM   #64
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Quote:
Originally Posted by narain View Post
So what is the update with this project https://github.com/nh13/samtools . Is it still faster than multi-threaded version of samtools ? Is this going to be a good substitute for Goby and Cram ?
There was no desire from the folks maintaining samtools to take over the development and add it. Sorry for the delayed response.
nilshomer is offline   Reply With Quote
Reply

Tags
sam, samtools

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 03:40 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO