recipe noise2read

Turn noise to read

Homepage:

https://github.com/Jappy0/noise2read

License:

MIT

Recipe:

/noise2read/meta.yaml

noise2read, originated in a computable rule translated from PCR erring mechanism that: a rare read is erroneous if it has a neighboring read of high abundance, turns erroneous reads into their original state without bringing up any non-existing sequences into the short read set(&lt 300bp) including DNA and RNA sequencing (DNA/RNA-seq), small RNA, unique molecular identifiers (UMI) and amplicon sequencing data.

package noise2read

versions:

0.3.0-0,  0.2.10-0,  0.2.7-0

depends bcool:

depends biopython:

1.79

depends editdistance:

>=0.6.0

depends imbalanced-learn:

>=0.9.1

depends matplotlib-base:

>=3.5.2

depends mpire:

>=2.8.0

depends networkx:

2.8.5

depends optuna:

>=3.1.1

depends pandas:

>=1.4.3

depends python:

>=3.8

depends scikit-learn:

>=1.1.1

depends seqtk:

depends xgboost:

1.6.1

depends xlsxwriter:

>=3.0.3

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 noise2read

and update with::

   mamba update noise2read

To create a new environment, run:

mamba create --name myenvname noise2read

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/noise2read:<tag>

(see `noise2read/tags`_ for valid values for ``<tag>``)

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