recipe mirtrace

miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum.

Homepage:

https://github.com/friedlanderlab/mirtrace

License:

GPL-2.0

Recipe:

/mirtrace/meta.yaml

Links:

biotools: mirtrace, doi: 10.1186/s13059-018-1588-9

package mirtrace

(downloads) docker_mirtrace

versions:

1.0.1-1,  1.0.1-0,  1.0.0-0

depends openjdk:

>=8.0.144

depends python:

requirements:

additional platforms:

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 mirtrace

and update with::

   mamba update mirtrace

To create a new environment, run:

mamba create --name myenvname mirtrace

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/mirtrace:<tag>

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

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