Lastz

Introduction

• An aligner that can map entire genomes to each other.
• Gapped Blast inspired Blastz, and Blastz inspired Lastz

Usage examples

Here we take align two entire chromosomes: chr4 from human and chicken get the output in MAF format.

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

We can also format the output for consumption by R, with the --format=rdotplot option.

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