recipe hiline

HiC alignment and classification pipeline.

Homepage

https://github.com/wtsi-hpag/HiLine

License

MIT / MIT

Recipe

/hiline/meta.yaml

This is a HiC short-read alignment pipeline. It will perform an alignment, or read in an external alignment, perform optional duplicate-read marking, perform HiC read classification based on an in-slico restriction digest of reference sequences and finally split the output alignments based on HiC read-type. It can also optionally process and output HiC alignment statistics. Under the hood, it uses bwa mem and samtools to perform and process alignments. It also uses a custom C++ Python extension to perform the in-silico digest (using the Hyperscan (https://github.com/intel/hyperscan) regex library) and subsequent HiC classification.

package hiline

Versions

0.2.4-1,  0.2.4-0,  0.2.2-1,  0.2.2-0,  0.2.1-0,  0.1-0,  0.0.9-3,  0.0.9-2,  0.0.9-1, 

0.2.4-1,  0.2.4-0,  0.2.2-1,  0.2.2-0,  0.2.1-0,  0.1-0,  0.0.9-3,  0.0.9-2,  0.0.9-1,  0.0.9-0,  0.0.8-0,  0.0.7-0,  0.0.6-0,  0.0.5-0,  0.0.3-0,  0.0.2-0,  0.0.1-0

Depends

• biopython >=1.76

• bwa >=0.7.17

• click >=7.0

• gawk >=5.1.0

• libcxx >=12.0.1

• matplotlib-base >=3.2.0

• minimap2 >=2.17

• numpy >=1.22.2,<2.0a0

• pandas >=1.0.1

• pcre >=8.45,<9.0a0

• perl >=5.30.3

• python >=3.9,<3.10.0a0

• python_abi 3.9.* *_cp39

• samtools >=1.10

• seaborn >=0.10.0

Required By

Installation

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

conda install hiline

and update with:

conda update hiline

or use the docker container:

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

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

Download stats

Link to this page

Render an 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/hiline/README.html)