recipe scanindel

ScanIndel is a python program to detect indels (insertions and deletions) from NGS data by re-align and de novo assemble soft clipped reads.

Homepage

https://github.com/cauyrd/ScanIndel

License

GPL3 / GNU General Public License v3 or later (GPLv3+)

Recipe

/scanindel/meta.yaml

package scanindel

(downloads) docker_scanindel

Versions

1.3-0

Depends bedtools

==2.17.0

Depends biopython

==1.64

Depends blat

Depends bwa

==0.7.12

Depends freebayes

==0.9.21.7

Depends numpy

Depends pysam

==0.7.7

Depends python

2.7*

Depends pyvcf

==0.6.7

Depends samtools

<=1.0

Depends scipy

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install scanindel

and update with:

conda update scanindel

or use the docker container:

docker pull quay.io/biocontainers/scanindel:<tag>

(see scanindel/tags for valid values for <tag>)

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/scanindel/README.html)