SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Alignment of resequenced population genome data to reference genome (A. lyrata) everestial General 8 02-16-2016 07:57 PM
Alignment to a set of custom reference sequences along with standard genome reference eeyun Bioinformatics 4 05-08-2013 05:06 PM
Create new Reference by merging SNV list with reference genome rdoan Bioinformatics 0 10-12-2012 08:17 AM
Targeted Genome Assembly for region poorly represented in reference genome? gumbos Bioinformatics 1 01-09-2012 05:01 PM
Reference genome for MAQ - split reference genome by chromosome or not? inesdesantiago Bioinformatics 4 02-18-2009 09:44 AM

Reply
 
Thread Tools
Old 01-26-2017, 08:51 AM   #1
jordi
Member
 
Location: València, Spain

Join Date: Apr 2009
Posts: 48
Default Nanopolish without reference genome

Hi all!
I am trying to correct raw MinION sequencing reads with nanopolish since nanocorrect seems to be deprecated.
However, during the nanopolish workflow found here an alignment to a reference genome seem to be compulsory. So, how to proceed with nanopolish lacking a reference genome? I mean, how to correct raw sequencing reads (or assembled reads) without the bam file obtained with bwa?
Any help will be really apreciated.
jordi is offline   Reply With Quote
Old 11-06-2017, 08:14 AM   #2
cstack
Member
 
Location: Florida, US

Join Date: May 2017
Posts: 12
Default

Quote:
Originally Posted by jordi View Post
Hi all!
I am trying to correct raw MinION sequencing reads with nanopolish since nanocorrect seems to be deprecated.
However, during the nanopolish workflow found here an alignment to a reference genome seem to be compulsory. So, how to proceed with nanopolish lacking a reference genome? I mean, how to correct raw sequencing reads (or assembled reads) without the bam file obtained with bwa?
Any help will be really apreciated.
I guess you could try an all-vs-all mapping (skipping self-mapping) -- I think that graphmap and minialign can do this and output the results in SAM/BAM format.
cstack is offline   Reply With Quote
Old 11-08-2017, 05:27 AM   #3
apredeus
Senior Member
 
Location: Bioinformatics Institute, SPb

Join Date: Jul 2012
Posts: 146
Default

There is a tool from Schatz lab called NanoCORR: http://schatzlab.cshl.edu/data/nanocorr/

I don't think it's used much though. Also, as far as I know, nanopolish is the only tool that uses fast5 information. Do you need just the nanopore reads, not the assembly?

I would then suggest making an assembly, correcting it with nanopolish, then aligning the reads to the assembly and extracting the result from the BAM file. Those won't really be "reads" but they will be read-like fragments of the polished genome, which is roughly equivalent to corrected reads.

Otherwise, if you also got the Illumina data, you can use Masurca and find the "mega-reads" it generates. Those are also long reads corrected using Illumina before the assembly.
apredeus is offline   Reply With Quote
Reply

Tags
bioinformatic, minion, oxford nanopore

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 07:49 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO