recipe sff2fastq

Extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output

Homepage:

https://github.com/indraniel/sff2fastq

License:

GPL / GPL-3

Recipe:

/sff2fastq/meta.yaml

Links:

biotools: sff2fastq

The program sff2fastq extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.

package sff2fastq

(downloads) docker_sff2fastq

versions:

0.9.2-1,  0.9.2-0

depends libgcc-ng:

>=4.9

requirements:

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 sff2fastq

and update with::

   mamba update sff2fastq

To create a new environment, run:

mamba create --name myenvname sff2fastq

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/sff2fastq:<tag>

(see `sff2fastq/tags`_ for valid values for ``<tag>``)

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