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Old 11-02-2015, 07:18 PM   #1
ymc
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Default Software to use Illumina reads for error correction?

I am using Pilon. Seems ok to me.

Are there better alternatives?

I am using 2x250 MiSeq for error correction. Is there a better read length and machine-chemistry combo?
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Old 11-03-2015, 01:19 PM   #2
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you use the short reads from illumina to correct Nanopore long reads?
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Old 11-03-2015, 10:51 PM   #3
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Originally Posted by mido1951 View Post
you use the short reads from illumina to correct Nanopore long reads?
Yeah, to be specific, I only try to correct the 2D reads
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Old 11-04-2015, 03:43 AM   #4
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the NanoCorr for oxford nanopore reads correction.
it is specific to the nanopore data.
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Old 11-06-2015, 04:51 PM   #5
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Thanks for your NanoCorr suggestion. Did you also try NaS? If so, how did it compare to NanoCorr? Its paper claims it can improve K12 genome to one mismatch per 100kbp.
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Old 11-06-2015, 05:15 PM   #6
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Yes, I have used and tested NaS but I have not tested NanoCorr. I can not compare them because I have not tested NanoCorr. You have to see the results of the two papers, they used the same K12 genome.
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Old 11-12-2015, 08:56 PM   #7
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Originally Posted by mido1951 View Post
Yes, I have used and tested NaS but I have not tested NanoCorr. I can not compare them because I have not tested NanoCorr. You have to see the results of the two papers, they used the same K12 genome.
Thank you very much for your reply.

I am trying NaS now. It seems to output fasta of corrected nanopore reads. How do I feed fasta to celera assembler which is expecting a fastq?
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Old 12-03-2015, 01:48 AM   #8
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I'm not sure that this is what you are interested in, but if you want to assemble Nanopore reads after error correction with Illumina, you can try SPAdes for hybrid assembly instead.
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Old 12-18-2015, 02:40 PM   #9
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do you have installed Nanocore?
I could not install it.
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Old 12-27-2015, 06:20 AM   #10
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I could run both NaS and nanocorr to completion. But the resulting corrected fasta couldn't be assembled to a single contig whereas the uncorrected fasta could be assembled into one contig that is 94% identical to the reference E coli K12 MG1655 genome.

I used SRR1030394 from SRA to correct the 2d reads downloaded from
http://www.cbcb.umd.edu/software/PBc...aOxford.tar.gz
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Old 12-27-2015, 06:35 AM   #11
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for me, I could not install Nanocorr.
I do not know the problem.
do you have any problems during installation ??
Thank you
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Old 12-27-2015, 06:23 PM   #12
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Quote:
Originally Posted by mido1951 View Post
for me, I could not install Nanocorr.
I do not know the problem.
do you have any problems during installation ??
Thank you
I don't have any problem. I just followed what was described in README.
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Old 01-03-2016, 12:22 PM   #13
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for NaS, I find not long reads corrected !!
NaS do long reads generated corrected? and where I find this file?
Thank you
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Old 01-04-2016, 07:16 PM   #14
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Quote:
Originally Posted by mido1951 View Post
for NaS, I find not long reads corrected !!
NaS do long reads generated corrected? and where I find this file?
Thank you
NaS_hqctg_reads.fa?
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