recipe n50

calculate N50 from FASTA/FASTQ files, producing both machine and human friendly outputs

Homepage:

http://metacpan.org/pod/Proch::N50

Documentation:

https://github.com/quadram-institute-bioscience/seqfu/wiki/n50

Developer docs:

https://github.com/quadram-institute-bioscience/seqfu/

License:

mit

Recipe:

/n50/meta.yaml

Links:

biotools: n50, doi: 10.3390/bioengineering8050059

a program to calculate size metrics of a FASTA (or FASTQ) file: minimum, maximum, average length, N50, N75, N90 and the area of the Nx curve (auN). Gzipped files are supported as input, and the output can be in compact, csv, tsv, json or screen friendly format.

package n50

versions:

1.5.8-0,  1.5.6-0,  1.5.5-0,  1.5.4-0,  1.5.0-0,  1.4.10-1,  1.4.10-0,  1.4.2-2,  1.4.2-1, 

1.5.8-0,  1.5.6-0,  1.5.5-0,  1.5.4-0,  1.5.0-0,  1.4.10-1,  1.4.10-0,  1.4.2-2,  1.4.2-1,  1.4.2-0,  1.4.1-0,  1.3.0-1,  1.3.0-0,  1.2.0-0,  1.0.0-0,  0.92-0,  0.90-0,  0.83-0,  0.82-0,  0.80-0,  0.60-3,  0.60-2,  0.60-1,  0.60-0

depends perl:

>=5.32.1,<6.0a0 *_perl5

depends perl-exporter:

depends perl-fastx-reader:

>=1.8.0

depends perl-file-which:

depends perl-getopt-long:

depends perl-json-pp:

depends perl-perlio-encoding:

depends perl-pod-usage:

depends perl-text-asciitable:

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 n50

and update with::

   mamba update n50

To create a new environment, run:

mamba create --name myenvname n50

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/n50:<tag>

(see `n50/tags`_ for valid values for ``<tag>``)

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