recipe umicollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI).

Homepage:

https://github.com/Daniel-Liu-c0deb0t/UMICollapse

License:

MIT / MIT

Recipe:

/umicollapse/meta.yaml

UMIs are a popular way to identify duplicate DNA/RNA reads caused by PCR amplification. This requires software for collapsing duplicate reads with the same UMI, while accounting for sequencing/PCR errors. This tool implements many efficient algorithms for orders-of-magnitude faster UMI deduplication than previous tools (UMI-tools, etc.), while maintaining similar functionality. This is achieved by using faster data structures with n-grams and BK-trees, along other techniques that are carefully implemented to scale well to larger datasets and longer UMIs. Users of UMICollapse have reported speedups from taking hours or days to run with a previous tool to taking only a few minutes with this tool with real datasets! doi 10.7717/peerj.8275.

package umicollapse

(downloads) docker_umicollapse

versions:

1.0.0-1,  1.0.0-0

depends openjdk:

>=17

depends python:

requirements:

Installation

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 umicollapse

and update with::

   mamba update umicollapse

To create a new environment, run:

mamba create --name myenvname umicollapse

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 quay.io/biocontainers/umicollapse:<tag>

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

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