recipe magicblast

NCBI BLAST next generation read mapper



Public Domain




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 (, 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:

package magicblast

(downloads) docker_magicblast



Required By:


With an activated Bioconda channel (see set-up-channels), install with:

conda install magicblast

and update with:

conda update magicblast

or use the docker container:

docker pull<tag>

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

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