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.

References:

• Boratyn GM, Thierry-Mieg J, Thierry-Mieg D, Busby B, Madden TL. (2019) Magic-BLAST, an accurate RNA-seq aligner for long and short reads. BMC Bioinformatics 20: 405. doi:10.1186/s12859-019-2996-x

• Magic-BLAST Main Site

• Module Name: magicblast (see the modules page for more information)
• Multithreaded using the -num_threads argument to magicblast.

Allocate an interactive session and run the program.
The following sample session (user input in bold) is based on cookbooks from the official documentation:

[user@biowulf]$ sinteractive --cpus-per-task 8
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load magicblast

[user@cn3144 ~]$ makeblastdb -in my_reference.fa -out my_reference -parse_seqids -dbtype nucl 
[user@cn3144 ~]$ magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db my_reference
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. magicblast.sh). For example:

#!/bin/bash
set -e
module load magicblast
test -n $SLURM_CPUS_PER_TASK || SLURM_CPUS_PER_TASK=2
magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db my_reference

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] magicblast.sh

Create a swarmfile (e.g. magicblast.swarm). For example:

cd sample1 && magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db /data/$USER/references/my_reference
cd sample2 && magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db /data/$USER/references/my_reference
cd sample3 && magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db /data/$USER/references/my_reference
cd sample4 && magicblast -num_threads $SLURM_CPUS_PER_TASK -query reads.fa -db /data/$USER/references/my_reference

Submit this job using the swarm command.

swarm -f magicblast.swarm [-g #] -t # --module magicblast