NAME
Alien::SeqAlignment::cutadapt - Find or install cutadapt
SYNOPSIS
Command line tool:
cutadapt (list of options);
DESCRIPTION
This distribution provides the python tool cutadapt so that it can be used by other Perl distributions that are on CPAN. It does this by first trying to detect an existing install of cutadapt on your system. If found it will use that. If it cannot be found, it will use the Python package installer pipx to download and install cutadapt in an isolated environment for each user.
SEE ALSO
- cutadapt
-
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3' sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but often you don't want them to be in your reads.
Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads.
- Alien
-
Documentation on the Alien concept itself.
- Alien::Base
-
The base class for this Alien.
- Alien::Build::Manual::AlienUser
-
Detailed manual for users of Alien classes.
AUTHOR
Christos Argyropoulos <chrisarg@gmail.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2024 by Christos Argyropoulos.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.