Fastaq

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For sequence_trim it is unclear what the format for trim_seqs should be

2

Apologies if this is extremely basic, I'm new to sequence data/file manipulations at this level. I've tried formatting the trim_seqs input file as a fasta, and as a plain text...

idwProxima

Hi there, I tried shredding my fasta sequences to fastq using fastaq module they were converted successfully to paired end sequences however, were not handled correctly by srst2. The output...

UzmaBasit

Hi, I realized `fastaq batch` woud be handy, aiming to split input files into batches of N entries per output array of files. For example, to split input FASTA file...

mmokrejs

Hi, it seems fastaq breaks on some lines. Second, could there be an option to keep the remainder sequence, instead of discarding it? ```$ fastaq to_perfect_reads contigs.fa contigs.perfect_reads_100xcoverage.fa 300 20...

mmokrejs

to_perfect_reads.py does not support inputs which have a description text after an identifier. It just blindly appends the numbers to whatever text is present on the line. If the line...

mmokrejs

Hello, I see that in commands you can reverse complement your sequences, I was wondering if there is a way to only reverse your sequences. Thank you!!

galud27

They were left unchanged before

andreyto

Ambiguous nucleotides are treated literally by sequence_trim. e.g. specifying AAAN to be trimmed will trim "AAAN" from sequence ends, but not "AAAA", "AAAC" etc. which is probably fair enough, but...

ChrisHIV

Nose, which the package depends on, will no longer be maintained in the future, and has had issue with newer Python versions. I switched the Gentoo package of Fastaq from...

TheChymera