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-slico digest (using the Hyperscan (https://github.com/intel/hyperscan) regex library) and subsequent HiC classification.

package hiline

(downloads) docker_hiline

Versions
0.0.9-20.0.9-10.0.9-00.0.8-00.0.7-00.0.6-00.0.5-00.0.3-00.0.2-0

0.0.9-20.0.9-10.0.9-00.0.8-00.0.7-00.0.6-00.0.5-00.0.3-00.0.2-00.0.1-0

Depends
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>)