Difference between revisions of "Lastz"
(Created page with "= Introduction = An aligner that can map entire genomes to each other.") |
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= Introduction = | = Introduction = | ||
| − | An aligner that can map entire genomes to each other. | + | * 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 | ||
Latest revision as of 17:24, 10 March 2017
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
