LASTZ is a tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. It is a drop-in replacement for BLASTZ, and is backward compatible with BLASTZ's command-line syntax.

LASTZ is designed to preprocess one sequence or set of sequences (which we collectively call the target) and then align several query sequences to it. The general flow of the program is like a pipeline: the output of one stage is the input to the next. The user can choose to skip most stages via command-line options; any stages that are skipped pass their input along to the next stage unchanged. Two of the stages, scoring inference and interpolation, are special in that they perform a miniature version of the pipeline within them.

References:

• Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University.

• LASTZ Main Site

• Module Name: LASTZ (see the modules page for more information)
• Single-threaded
• Reference data in /data/genome/fasta/

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 ~]$ lastz hg18.chr4.fa galGal3.chr4.fa --notransition --step=20 --nogapped --format=maf > hg18_4_vs_galGal3_4.maf 

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

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

#!/bin/bash
set -e
module load LASTZ
lastz hg18.chr4.fa galGal3.chr4.fa --notransition --step=20 --nogapped --format=maf > hg18_4_vs_galGal3_4.maf

Submit this job using the Slurm sbatch command.

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

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

lastz hg18.chr1.fa galGal3.chr1.fa --notransition --step=20 --nogapped --format=maf > hg18_1_vs_galGal3_1.maf
lastz hg18.chr2.fa galGal3.chr2.fa --notransition --step=20 --nogapped --format=maf > hg18_2_vs_galGal3_2.maf
lastz hg18.chr3.fa galGal3.chr3.fa --notransition --step=20 --nogapped --format=maf > hg18_3_vs_galGal3_3.maf
lastz hg18.chr4.fa galGal3.chr4.fa --notransition --step=20 --nogapped --format=maf > hg18_4_vs_galGal3_4.maf

Submit this job using the swarm command.

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