NAME

fu-len - A demo implementation to filter fastx files by length

VERSION

version 1.5.0

USAGE

  fqlen [options] FILE1 FILE2 ... FILEn

PARAMETERS

-m, --min INT

Minimum length to print a sequence

-x, --max INT

Maximum length to print a sequence

-l, --len

Add read length as comment

-f, --fasta

Force FASTA output (default: as INPUT)

-w, --fasta-width INT

Paginate FASTA sequences (default: no)

-n, --namescheme

Sequence name scheme: "file" (Use file basename as prefix), "num" (Numbered sequence (see also -p)) and "raw" (Do not change sequence name, default)

-p, --prefix STR

Use as sequence name prefix this string

-c, --strip-comment

Remove sequence comment (default: no)

LIMITATIONS

Note that usage with multiple files can raise errors (eg. duplicate sequence name). Also, wrong formatting if mixing fasta and fastq files without specifying --fasta.

We recommend considering SeqFu to overcome these limitations: https://github.com/telatin/seqfu2.

CITING

Telatin A, Fariselli P, Birolo G. SeqFu: A Suite of Utilities for the Robust and Reproducible Manipulation of Sequence Files. Bioengineering 2021, 8, 59. https://doi.org/10.3390/bioengineering8050059

AUTHOR

Andrea Telatin <andrea@telatin.com>

COPYRIGHT AND LICENSE

This software is Copyright (c) 2018-2022 by Andrea Telatin.

This is free software, licensed under:

  The MIT (X11) License