Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.

References:

• Heng Li; Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, , bty191, doi:10.1093/bioinformatics/bty191

• minimap2 main site
• minimap2(1)

• Module Name: minimap2 (see the modules page for more information)
• environment variables set
  • MINIMAP2_HOME
• Example files in $MINIMAP2_HOME/test and /fdb/minimap2

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

[user@biowulf]$ sinteractive
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 minimap2
[+] Loading minimap2, version 2.2...
[user@cn3144 ~]$ man minimap2 # read the documentation
[user@cn3144 ~]$ minimap2 -ax map10k $MINIMAP2_HOME/test/MT-human.fa $MINIMAP2_HOME/test/MT-orang.fa > test.sam
[M::mm_idx_gen::0.005*1.16] collected minimizers
[M::mm_idx_gen::0.007*1.24] sorted minimizers
[M::main::0.007*1.24] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.008*1.19] mid_occ = 3
[M::mm_idx_stat] kmer size: 19; skip: 10; is_HPC: 1; #seq: 1
[M::mm_idx_stat::0.008*1.27] distinct minimizers: 2127 (99.95% are singletons); average occurrences: 1.000; average spacing: 7.786
[M::worker_pipeline::0.035*1.03] mapped 1 sequences
[M::main] Version: 2.2-r409
[M::main] CMD: minimap2 -ax map10k /usr/local/apps/minimap2/2.2/test/MT-human.fa /usr/local/apps/minimap2/2.2/test/MT-orang.fa
[M::main] Real time: 0.036 sec; CPU: 0.037 sec
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. minimap2.sh). For example:

#!/bin/bash
set -e
module load minimap2
minimap2 -ax map10k $MINIMAP2_HOME/test/MT-human.fa $MINIMAP2_HOME/test/MT-orang.fa > test.sam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] minimap2.sh

Create a swarmfile (e.g. minimap2.swarm). For example:

minimap2 -ax map10k reference.fa reads1.fa > out1.sam
minimap2 -ax map10k reference.fa reads2.fa > out2.sam
minimap2 -ax map10k reference.fa reads3.fa > out3.sam
minimap2 -ax map10k reference.fa reads4.fa > out4.sam

Submit this job using the swarm command.

swarm -f minimap2.swarm [-g #] [-t #] --module minimap2