SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
NGS Analysis pipeline comparison MenzZana Bioinformatics 2 02-04-2013 12:41 AM
quality score of 41 from illumina 1.5 pipeline? yjx1217 Bioinformatics 2 09-25-2012 07:05 PM
QC of NGS analysis pipeline? mzpitman Bioinformatics 8 02-22-2012 03:11 PM
Offering a user-paid NGS analysis pipeline in the cloud schelhorn Bioinformatics 0 08-25-2011 02:04 AM
Managing Your NGS Pipeline Workshop Pavolga Events / Conferences 0 04-21-2011 07:53 AM

Reply
 
Thread Tools
Old 03-12-2014, 01:48 AM   #1
Nilaksha
Member
 
Location: Sri Lanka

Join Date: Mar 2014
Posts: 19
Default Validating and Evaluating the Quality of an NGS pipeline

Hello all, I'm a novice bioinformatician and have developed a NGS analysis pipeline majorly for SNP calling. I would like to evaluate the accuracy of my pipeline either against a set of genotyped SNP list or a simulated reading. I have already looked at wgsim tool, which is pretty impressive but I got doubts with the parameters of wgsim_eval.pl which are explained nowhere, even in their read me files. Any help or suggestion would be much appreciated.

Thanks

UPDATE: I found the parameter definitions for wgsim_eval.pl, they are already included in the seperate wgsim package which is not an integration of samtools, in which I found no information.

Last edited by Nilaksha; 03-12-2014 at 02:10 AM.
Nilaksha is offline   Reply With Quote
Old 03-12-2014, 05:17 AM   #2
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

We have used stampy's built in read simulation tool. It is well documented.
TiborNagy is offline   Reply With Quote
Old 03-12-2014, 08:24 PM   #3
Nilaksha
Member
 
Location: Sri Lanka

Join Date: Mar 2014
Posts: 19
Default

Thanks a lot for the answer. I will read up more on that and let you know the progress
Nilaksha is offline   Reply With Quote
Reply

Tags
evaluating ngs pipeline, wgsim

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 04:38 AM.


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