Tool:A pairwise genome alignment pipeline using LAST and Nextflow
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8 weeks ago
Charles Plessy ★ 2.7k

I have prepared a pairwise genome alignment pipeline for Nextflow and plan to submit it to nf-core as a standalone pipeline or a subworkflow.

Using tools from the LAST suite, it takes genomes in FASTA format, trains itself to find the best alignment parameters, aligns the genomes, reduces the result to a set one-to-one matches and produces a dotplot. Alignment files and dotplots for the intermediate steps (many-to-many and one-to-many) are also provided. It can align many query genomes to a single target genome (the one that will be indexed) in parallel.

I use it routinely on small genomes and trust it. If you find it useful or find issues, I would welcome your comments.

https://github.com/oist/plessy_pairwiseGenomeComparison

Readers in the future, please note that the URL will eventually change when the pipeline will be finalised.

genome LAST Nextflow dotplot alignment • 117 views
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