Miniprot aligns protein sequences to whole genomes with splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.

References:

• Li, H. Protein-to-genome alignment with miniprot. Bioinformatics, 39, btad014

• miniprot Main Site

• Module Name: miniprot (see the modules page for more information)
• Multithreaded via the -t flag.
• Environment variables set
  • MINIPROT_HOME
• Example files in $MINIPROT_HOME/test

Allocate an interactive session and run the program.
Sample session (user input in bold):

[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 miniprot
[+] Loading miniprot, version 0.13...
[user@cn3144 ~]$ man miniprot # Read the manual (Press q to exit it once finished)
[user@cn3144 ~]$ miniprot --gff $MINIPROT_HOME/test/DPP3-hs.gen.fa.gz $MINIPROT_HOME/test/DPP3-mm.pep.fa.gz > aln.gff

[M::mp_ntseq_read@0.005*0.34] read 27033 bases in 1 contigs
[M::mp_idx_build@0.005*0.35] 212 blocks
[M::mp_idx_build@0.006*0.62] collected syncmers
[M::mp_idx_build@0.046*0.94] 16125 kmer-block pairs
[M::mp_idx_print_stat] 14397 distinct k-mers; mean occ of infrequent k-mers: 1.12; 0 frequent k-mers accounting for 0 occurrences
[M::worker_pipeline::0.063*0.85] mapped 1 sequences
[M::main] Version: 0.13-r248
[M::main] CMD: miniprot --gff /usr/local/apps/miniprot/0.13/test/DPP3-hs.gen.fa.gz /usr/local/apps/miniprot/0.13/test/DPP3-mm.pep.fa.gz
[M::main] Real time: 0.067 sec; CPU: 0.057 sec; Peak RSS: 0.067 GB
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load miniprot
miniprot -t 2 $MINIPROT_HOME/test/DPP3-hs.gen.fa.gz $MINIPROT_HOME/test/DPP3-mm.pep.fa.gz > aln.paf

Submit this job using the Slurm sbatch command.

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

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

miniprot -t $SLURM_CPUS_PER_TASK -Iut16 --gff genome.fna sample1.faa > sample1.aln.gff
miniprot -t $SLURM_CPUS_PER_TASK -Iut16 --gff genome.fna sample2.faa > sample2.aln.gff
miniprot -t $SLURM_CPUS_PER_TASK -Iut16 --gff genome.fna sample3.faa > sample3.aln.gff
miniprot -t $SLURM_CPUS_PER_TASK -Iut16 --gff genome.fna sample4.faa > sample4.aln.gff

Submit this job using the swarm command.

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