Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
New alignment algorithm in the works, feedback needed! Dakduif Bioinformatics 0 05-07-2013 06:42 AM
Are there any alignment programs that take SNPs into account during alignment? sdarko Bioinformatics 2 06-04-2011 06:09 AM
Online Bisulfite Alignment programs? hxm44 Bioinformatics 4 05-18-2011 05:11 PM
Preliminary benchmark of different alignment programs lh3 Bioinformatics 33 12-13-2009 03:23 PM
Alignment programs comparison bioxyz Bioinformatics 0 11-25-2009 04:33 PM

Thread Tools
Old 02-18-2019, 10:35 AM   #1
Junior Member
Location: Canada

Join Date: Feb 2019
Posts: 1
Default Feedback on Read Alignment Programs

Hey everyone! I'm a microbiology undergrad in the middle of completing a work term with a bioinformatics team. My project for the semester involves researching different read alignment / mapping programs for the development of a future training course. One point that's been emphasized is that I should look into the effects of using the default parameters vs custom settings.

So far, I've been looking into Bowtie2, BWA and BWA-MEM, SMALT, segemehl, and BBMap. Reading the manuals and literature, trying to get a few test datasets, figuring out the different options for each program. I've also just added Minimap2 to my list, and will be reading up on that one over the coming days.

If you perform read alignments as part of your research, or have any other unique expertise on the subject, I'd be grateful for whatever insight you can offer! Here's an idea of the type of questions I'd like feedback on:
  • What sequencing technology do you use to obtain your reads? What is your preferred tool for performing read alignments, and why? What advantage does it have over other available programs?
  • Are there any unique challenges presented by the organisms you study or the sequencing technology you use? What adjustments do you make to your workflow to combat this?
  • What factors do you place the most weight on when performing read alignments? Speed, adjustable parameters, low memory requirements?
  • Do you use default settings, or custom options? If you use custom settings, what options do you change? Why is this necessary? How does it affect the outcome of your alignment?
  • Any other info you think is valuable and would like to share with me!

Thanks in advance!
Mach2 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 01:18 AM.

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