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