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splatlab / squeakr

Squeakr: An Exact and Approximate k -mer Counting System
BSD 3-Clause "New" or "Revised" License
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Plans to support FASTA? #31

Open hmusta opened 6 years ago

hmusta commented 6 years ago

Are there any plans to support FASTA files any time in the future?

Given a FASTA file as input, would it be sufficient to reformat it as a FASTQ file by flattening multi-line sequences to a single line and adding dummy quality scores?

prashantpandey commented 5 years ago

Hi @hmusta , yes. You can do that. We just tried this approach in one of our other projects and it worked.

Thanks, Prashant

tseemann commented 5 years ago

You can to this efficiently using seqtk seq -F 40 -U file.fa.gz > file.fq