recipe biopet-seqstat

SeqStat is a package that contains tools to generate stats from a FastQ file, merge those stats for multiple samples, and validate the generated stats files.

Homepage:

https://github.com/biopet/seqstat

License:

MIT

Recipe:

/biopet-seqstat/meta.yaml

SeqStat is a package that contains tools to generate stats from a FastQ file, merge those stats for multiple samples, and validate the generated stats files.

#### Mode - Generate

Generate outputs several stats on a FASTQ file.

Outputted stats:

- Bases

- Total number - Base qualities, with the number of bases having that quality - Number of each nucleotide

- Reads

- Total number - minimum length - maximum length - A histogram of the average base qualities - The quality encoding (Sanger, solexa etc.) - A histogram of the read lengths.

#### Mode - Merge

This module will merge seqstat files together and keep the sample/library/readgroup structure. If required it's also possible to collapse this, the output file then des not have any sample/library/readgroup structure.

#### Mode - Validate

A file from SeqStat will validate the input files. If aggregation values can not be regenerated the file is considered corrupt. This should only happen when the user will edit the seqstat file manually.

For documentation and manuals visit our github.io page: https://biopet.github.io/seqstat

package biopet-seqstat

(downloads) docker_biopet-seqstat

versions:

1.0.1-1,  1.0.1-0,  1.0-1,  1.0-0,  0.1-2,  0.1-1,  0.1-0

depends openjdk:

>=8,<9

depends python:

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 biopet-seqstat

and update with::

   mamba update biopet-seqstat

To create a new environment, run:

mamba create --name myenvname biopet-seqstat

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/biopet-seqstat:<tag>

(see `biopet-seqstat/tags`_ for valid values for ``<tag>``)

Notes

biopet-seqstat is a Java program that comes with a custom wrapper shell script. By default 'no default java option' is set in the wrapper. The command that runs the program is 'biopet-seqstat'. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with 'biopet-seqstat -Xms512m -Xmx1g'.

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/biopet-seqstat/README.html)