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Advice for generating simplitigs from FASTQ files #12

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SionBayliss opened this issue Oct 7, 2020 · 0 comments
Open

Advice for generating simplitigs from FASTQ files #12

SionBayliss opened this issue Oct 7, 2020 · 0 comments

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@SionBayliss
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Apologies. This is a question I emailed to you, but it maybe of use to other users if posted here

I would be interested in generating simplitigs from fastq files. This raises a few questions:

1/ As ProPhasm does not accept fastq files would it be suitable to convert the reads directly to fasta or to k-mers before passing to ProPhasm?
2/ There are many potential sources of error/noise in raw reads so would you recommend pre-processing K-mers (filtering/correcting) before passing to ProPhasm?
3/ Would native frequency filtering be something you would consider instituting in the software?
4/ A K-mer size of 32 bp is the maximum allowed for the '-k' option. Could this be relaxed to allow for assembly with larger K-mers and how might this be achieved?

Thanks for your help!

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