Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

Minialign is a little bit fast and moderately accurate nucleotide sequence alignment tool designed for PacBio and Nanopore long reads. It is built on three key algorithms, minimizer-based index of the minimap overlapper, array-based seed chaining, and SIMD-parallel Smith-Waterman-Gotoh extension.

References:

• See https://github.com/ocxtal/minialign

• https://github.com/ocxtal/minialign

• Module Name: minialign (see the modules page for more information)
• Multithreaded

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=4 
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 minialign
[user@cn3144 ~]$ minialign -t 4 ref.fa input.fa > out.sam
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load minialign
minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam

Submit this job using the Slurm sbatch command.

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

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

cd dir1; minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam
cd dir2; minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam
cd dir3; minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam
cd dir4; minialign -t $SLURM_CPUS_PER_TASK ref.fa input.fa > out.sam

Submit this job using the swarm command.

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

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
--module	Loads the module for each subjob in the swarm