Software to use Illumina reads for error correction?

[ymc]

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?

[mido1951]

you use the short reads from illumina to correct Nanopore long reads?

[ymc]

you use the short reads from illumina to correct Nanopore long reads?

Yeah, to be specific, I only try to correct the 2D reads

[mido1951]

the NanoCorr for oxford nanopore reads correction.
it is specific to the nanopore data.

[ymc]

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.

[mido1951]

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.

[ymc]

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?

[Dmitry.Antipov]

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.

[mido1951]

do you have installed Nanocore?
I could not install it.

[ymc]

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/PBcR/data/sampleDataOxford.tar.gz

[mido1951]

for me, I could not install Nanocorr.
I do not know the problem.
do you have any problems during installation ??
Thank you

[ymc]

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.

[mido1951]

for NaS, I find not long reads corrected !!
NaS do long reads generated corrected? and where I find this file?
Thank you

[ymc]

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?