---
name: "normalisefasta"
section: "1"
platform: "linux"
package: "biobambam2"
version: "2.0.185+ds-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/normalisefasta"
---

# normalisefasta(1)

normalise line length in a FastA file

## NAME

normalisefasta - normalise line length in a FastA file

## SYNOPSIS

**normalisefasta** \[options\]

## DESCRIPTION

normalisefasta reads a FastA file from standard input and outputs a reformatted version of the file with a consistent length of the lines containing sequence information on standard output. The program can either produce uncompressed or BGZF compressed output. For uncompressed output a FastA index (.fai) is produced on the standard error channel.

The following key=value pairs can be given:

**cols=\<\[80\]\>** line width for the lines containing sequence information in number of bases. This option is only considered for uncompressed output (i.e. bgzf=0)

**bgzf=\<0\|1\>** produce uncompressed (bgzf=0) or compressed (bgzf=1) output

**index=\<\>** if bgzf=1 this key can be used for giving the file name for the index file allowing (pseudo) random access in the output file. If the key is not given when bgzf=1, then no index is written.

**level=\<-1\|0\|1\|9\|11\>:** set compression level of the output file if bgzf=1. Valid values are

- \-1:

  zlib/gzip default compression level

- 0:

  uncompressed

- 1:

  zlib/gzip level 1 (fast) compression

- 9:

  zlib/gzip level 9 (best) compression

If libmaus has been compiled with support for igzip (see https://software.intel.com/en-us/articles/igzip-a-high-performance-deflate-compressor-with-optimizations-for-genomic-data) then an additional valid value is

- 11:

  igzip compression

**minlength=\<\[0\]\>** Minimum length. Reads shorter than this will be discarded. By default all reads are kept.

## AUTHOR

Written by German Tischler.

## REPORTING BUGS

Report bugs to \<germant@miltenyibiotec.de\>

## COPYRIGHT

Copyright © 2009-2014 German Tischler, © 2011-2014 Genome Research Limited. License GPLv3+: GNU GPL version 3 \<http://gnu.org/licenses/gpl.html\>\
 This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.