Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Using SNP/Indel Callers with 454 adaptivegenome Bioinformatics 6 05-18-2012 02:13 PM
suitable tools for hetero SNP/INDEL discovery? shuang Bioinformatics 0 10-04-2011 09:18 AM
Pileup - Filter SNP/Indel linked to 454 homopolymer bardou Bioinformatics 0 06-30-2010 08:17 AM
Running MAQ SNP/Indel detection/Assembly Tools on short aligners zee Bioinformatics 4 12-11-2009 02:41 PM
Next Gene Software for Solexa - SNP Indel detection EdK General 2 10-06-2009 09:51 AM

Thread Tools
Old 03-05-2009, 06:23 AM   #1
Junior Member
Location: Amsterdam, NL

Join Date: Feb 2009
Posts: 5
Question Comparing SNP/indel detection tools on 454

Hi everybody,

I'm quite new to the field of sequencing and working on a project to find out which software we can use best to detect SNP's and indels using a recently bought 454.
So far I have compiled a small incomplete list of which tools to look at, but these are mostly limited to separate SNP detection tools. I think it is mostly lacking integrated solutions or software packages which also have SNP/indel detection applications besides alignment and/or assembly capabilities.

My list so far:

Seperate tools:



454 software package
CLCbio Genomics Workbench
SeqMan Ngen

Is it perhaps wise to include alternative base-callers in the comparison as well?

I would be very happy to get any suggestions or tips from people working on 454 data as well.

Thank you for your time and input,

dePhi is offline   Reply With Quote
Old 03-05-2009, 09:18 AM   #2
Location: belgium

Join Date: Dec 2008
Posts: 52

my experience with the state of the art software is, they all lack something.

Especially the 454 software is not good for resequencing purposes. The AVA software is not able to decently detect gaps/inserts/indels.

Also the mapping software is not very good.

But i understand the manufacturers. Everybody is doing very different experiments, it is difficult to generate a working broad software platform. For general resequencing experiments, the AVA is ok.

For example finding differences in a yeast strain, AVA is ok.

But for analysing complex multiplex amplicon sequencing experiments, AVA is not what you need. In fact, nothing is what you need. You will have to design your own pipeline, design your own database probably if you want to compare different runs with each other etc etc.

The data analysis is not what it should be. We used the sequencer to analyse the PCR efficiency and primer mismatches in the multiplex. I am quite sure no standard package has that kind of software or analyses. But when you design your own databases and use a simple program as BLAT you can get great results to optimize your PCR reactions. We reduced erronouos pcr products from 22% to 4-5% of the total sequence pool in.

Conclusion: You will need a bunch of informatics/servers to analyse your sequencing data properly!
joa_ds is offline   Reply With Quote
Old 03-07-2009, 05:41 AM   #3
Junior Member
Location: Amsterdam, NL

Join Date: Feb 2009
Posts: 5

Cheers mate, thx for the input!

I was already getting the feeling that this isn't going to be the "small project" we thought it would be.
Ah well, here we go!
dePhi is offline   Reply With Quote

454, compare, indel, snp

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 02:44 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO