- recipe hiline
HiC alignment and classification pipeline.
- Homepage:
- License:
MIT / MIT
- Recipe:
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:
- Required By:
Installation
With an activated Bioconda channel (see 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:
[](http://bioconda.github.io/recipes/hiline/README.html)