- recipe rnaquast
rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
- Homepage:
- License:
GPL / GPL-2.0-or-later
- Recipe:
- Links:
doi: 10.1093/bioinformatics/btw218, biotools: rnaQUAST, usegalaxy-eu: rna_quast
- package rnaquast¶
- versions:
2.3.0-0,2.2.3-0,2.2.1-0,2.2.0-2,2.2.0-1,2.2.0-0,2.1.0-1,2.1.0-0,2.0.1-0,2.3.0-0,2.2.3-0,2.2.1-0,2.2.0-2,2.2.0-1,2.2.0-0,2.1.0-1,2.1.0-0,2.0.1-0,2.0.0-0,1.5.1-0- depends blast:
- depends busco:
>=5- depends emboss:
- depends gffutils:
- depends gmap:
>=2020.03.12- depends joblib:
- depends matplotlib-base:
- depends python:
- depends samtools:
- depends star:
- depends ucsc-blat:
- depends ucsc-pslsort:
- 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 rnaquast and update with:: mamba update rnaquast
To create a new environment, run:
mamba create --name myenvname rnaquast
with
myenvnamebeing 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/rnaquast:<tag> (see `rnaquast/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/rnaquast/README.html)
