recipe perl-fastx-abi

FASTX::Abi - Read Sanger trace file (.ab1 chromatograms) in FASTQ format. For traces called with hetero option, the ambiguities will be split into two sequences to allow usage from NGS tools that usually do not understand IUPAC ambiguities.

Homepage:

https://github.com/telatin/FASTX-Abi

Documentation:

https://metacpan.org/pod/FASTX::Abi

License:

MIT

Recipe:

/perl-fastx-abi/meta.yaml

This module reads a Sanger trace (chromatogram). If the chromatogram was saved in "hetero" mode, that is allowing IUPAC ambiguities in the basecalling, the module will return two (unphased) sequences in standard "ACGT" alphabet.

package perl-fastx-abi

(downloads) docker_perl-fastx-abi

versions:

1.0.1-1,  1.0.1-0,  1.0.0-0,  0.11-1,  0.11-0,  0.08-0

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-bio-trace-abif:

depends perl-carp:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install perl-fastx-abi

and update with::

   mamba update perl-fastx-abi

To create a new environment, run:

mamba create --name myenvname perl-fastx-abi

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/perl-fastx-abi:<tag>

(see `perl-fastx-abi/tags`_ for valid values for ``<tag>``)

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