Go Back   SEQanswers > Sequencing Technologies/Companies > 454 Pyrosequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Using solexa to correct 454 homopolymer errors coldturkey Bioinformatics 21 01-26-2016 01:39 AM
Pileup - Filter SNP/Indel linked to 454 homopolymer bardou Bioinformatics 0 06-30-2010 07:17 AM
454 homopolymer error rate joa_ds 454 Pyrosequencing 10 12-18-2009 10:33 AM
454 sequencing data coverage Salmon 454 Pyrosequencing 4 02-05-2009 01:18 PM
454 homopolymer errors or???? ian Adams 454 Pyrosequencing 9 12-02-2008 01:46 AM

Thread Tools
Old 01-22-2009, 08:13 AM   #1
Junior Member
Location: az

Join Date: Jan 2009
Posts: 9
Default Homopolymer error in 454 sequencing data

I am currently working on genome assembly. our reads data is from 454 sequencing. First we assembled contigs using Newbler. However, when we compared our built genome with a reference genome (very close relationship), we found several genes were separated into two or three pieces because of the frame shift. After checked the reads data and reference data, we think it may cause by homopolymer errors because homopolymer error is very common in 454 sequencing data.
In order to solve the homopolymer problem, should I re-assemble reads data using other assembler such as MIRA? Or does anyone give us some suggestions on homopolymer error?
Salmon is offline   Reply With Quote
Old 01-23-2009, 05:40 AM   #2
Junior Member
Location: USA

Join Date: Sep 2008
Posts: 6

A commercial assembly tool that may help is one from DNASTAR called SeqMan NGen. It avoids some of the issues related to homopolymeric errors seen in other assemblers. If you contact the company you can also get their technical support people to help determine if the issue is related to this or some other issue as you are evaluating the software.
rs705 is offline   Reply With Quote
Old 01-29-2009, 05:53 AM   #3
Location: Germany

Join Date: Jan 2009
Posts: 41

I have compared their results, Seqman can solve the problem to a certain degree, although it causes other problem in my data.
mingkunli is offline   Reply With Quote
Old 02-06-2009, 09:08 AM   #4
Location: konstanz

Join Date: Feb 2009
Posts: 10

hi, i don't think MIRA will do a better job, since the contigs(454 raw reads) i am analysing were assembled by MIRA, i also find some contigs are extremely similar, the differences are always found in the homopolymer region. 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 06:17 AM.

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