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

(downloads) docker_magicblast

Versions:

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

Depends:

  • on bzip2 >=1.0.8,<2.0a0

  • on libgcc-ng >=12

  • on libstdcxx-ng >=12

  • on libxml2 >=2.9.14,<2.10.0a0

  • on libzlib >=1.2.13,<1.3.0a0

  • on zlib >=1.2.13,<1.3.0a0

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 magicblast

to add into an existing workspace instead, run:

pixi add magicblast

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 magicblast

Alternatively, to install into a new environment, run:

conda create -n envname magicblast

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/magicblast:<tag>

(see magicblast/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.

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