LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:

• Finding rearrangements and recombinations (last-split)
• Finding DNA-versus-protein related regions, especially protein fossils.
• Unusual data, e.g. AT-rich DNA, because it can fit parameters to the data and calculate significance.
• Sensitive DNA-DNA search, due to fitting, sensitive seeding, and calculating significance.

References:

• Kiełbasa SM, Wan R, Sato K, Horton P, Frith MC. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011 21(3):487-93.
• See Detailed papers on LAST for a full list.

• LAST Main Site
• LAST Cookbook
• Documentation page listing

• Module Name: last (see the modules page for more information)
• Multithreaded using the -P flag on lastal
• Environment variables set
  • LAST_HOME
• Example files in $LAST_HOME/examples

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 last

[user@cn3144 ~]$ lastdb humdb $LAST_HOME/examples/humanMito.fa
[user@cn3144 ~]$ lastal humdb $LAST_HOME/examples/fuguMito.fa > myalns.maf

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load last
lastdb humdb $LAST_HOME/examples/humanMito.fa
lastal humdb $LAST_HOME/examples/fuguMito.fa > myalns.maf

Submit this job using the Slurm sbatch command.

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

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

lastal -P $SLURM_CPUS_PER_TASK humdb sample1.fa > s1.maf
lastal -P $SLURM_CPUS_PER_TASK humdb sample2.fa > s2.maf
lastal -P $SLURM_CPUS_PER_TASK humdb sample3.fa > s3.maf
lastal -P $SLURM_CPUS_PER_TASK humdb sample4.fa > s4.maf

Submit this job using the swarm command.

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