recipe hiline

HiC alignment and classification pipeline.






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 ( regex library) and subsequent HiC classification.

package hiline

(downloads) docker_hiline



depends biopython:


depends bwa:


depends click:


depends gawk:


depends libcxx:


depends matplotlib-base:


depends minimap2:


depends numpy:


depends pandas:


depends pcre:


depends perl:


depends python:


depends python_abi:

3.9.* *_cp39

depends samtools:


depends seaborn:




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 hiline

and update with::

   mamba update hiline

To create a new environment, run:

mamba create --name myenvname hiline

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<tag>

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

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