recipe magicblast

NCBI BLAST next generation read mapper

Homepage:

https://ncbi.github.io/magicblast/

License:

Public Domain

Recipe:

/magicblast/meta.yaml

Links:

biotools: magicblast, doi: 10.1186/s12859-019-2996-x

Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

More details about the algorithm and comparison with other similar tools are presented here: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2996-x.

package magicblast

versions:

1.7.0-0,  1.6.0-1,  1.6.0-0,  1.5.0-0,  1.4.0-0

depends bzip2:

>=1.0.8,<2.0a0

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libxml2:

>=2.9.14,<2.10.0a0

depends libzlib:

>=1.2.13,<1.3.0a0

depends zlib:

>=1.2.13,<1.3.0a0

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 magicblast

and update with::

   mamba update magicblast

To create a new environment, run:

mamba create --name myenvname magicblast

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/magicblast:<tag>

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

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