Package Recipe 'noise2read'

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:

on bcool
on biopython 1.79
on editdistance >=0.6.0
on imbalanced-learn >=0.9.1
on matplotlib-base >=3.5.2
on mpire >=2.8.0
on networkx 2.8.5
on optuna >=3.1.1
on pandas >=1.4.3
on python >=3.8
on scikit-learn >=1.1.1
on seqtk
on xgboost 1.6.1
on xlsxwriter >=3.0.3

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install noise2read

to add into an existing workspace instead, run:

pixi add noise2read

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install noise2read

Alternatively, to install into a new environment, run:

conda create -n envname noise2read

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/noise2read:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/noise2read/README.html)