Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Software to use Illumina reads for error correction? ymc Oxford Nanopore 13 01-04-2016 08:16 PM
Desperate grad student trying to correct pacbio reads with illumina data LampreyGuy Pacific Biosciences 11 10-29-2015 05:38 PM
LSC - a fast PacBio long read error correction tool. LSC Bioinformatics 9 08-21-2015 07:06 AM
Error correction on PacBio with illumina and 454 lucio89 Pacific Biosciences 0 10-03-2014 05:13 PM
pacbio sequence error correction Pacific Biosciences 5 11-22-2012 09:17 AM

Thread Tools
Old 01-27-2016, 07:50 PM   #1
Location: St. Louis

Join Date: Dec 2009
Posts: 74
Default Problems running nanocorr error correction w/ illumina reads and pacbio data

I have an assembly of a nematode genome (~410Mb in size) that was originally created from 454 data, and then later improved with PacBio data using PBJelly. I would now like to try and error correct this data using 30x coverage of Illumina reads and the NANOCORR software, but I'm having some trouble understanding how to run it.

Looking at the README, I see that I am supposed to run a partition script on what would be the nanopre_reads, but in my case I don't have that. The reads I want to use to improve my assembly are Illumina reads. So should I be partitioning the Illumina reads instead?

Then, the actual nanocorr command line is basically this: query.fa reference.fa

and the software README says:
The query file will be "blasted" against each previously partitioned read.
This query file can be anything useful for correction.
Illumina data is what is used right now.

So this is what confuses me. I know the typical usage of nanocorr would be to have nanopore reads, illumina reads, and a reference. In my case I have only an assembly that I want to error correct, and illumina reads. Technically I also have PacBio data, but I have already improved my assembly using that data via PBJelly. I just want to error correct this assembly using the illumina data. Can nanocorr help me in this case? A co-worker who recently left said he had been using nanocorr to do this kind of thing, but when I look at it, it seems like this is not the typical usage. And the documentation he left behind is not very complete.

If anybody here has experience with nanocorr I'd really appreciate some advice.

jmartin is offline   Reply With Quote
Old 01-28-2016, 01:03 PM   #2
Senior Member
Location: San Francisco

Join Date: Aug 2012
Posts: 322

Try which was designed for this task.
rhall 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 11:10 AM.

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