nextflow LiftOver workflow

nf-LO is a nextflow workflow for generating genome alignment files compatible with the UCSC liftOver utility for converting genomic coordinates between assemblies. It can automatically pull genomes directly from NCBI or iGenomes (or the user can provide fasta files) and supports four different aligners (lastz, blat, minimap2, GSAlign). Together these provide solutions for both different-species (lastz and minimap2) as well as same-species alignments (blat and GSAlign), with both standard and ultra-fast algorithms from a source to a target genome. It comes with a series of presets, allowing alignments of genomes depending on their genomic distance (near, medium and far).

Updates

UPDATE 14/12/2022: Now the NCBI/iGenomes accession have to be provided in the –source/–target field, and then use the appropriate –igenomes_source/–ncbi_source and –igenomes_target/–ncbi_target as a modifier.

UPDATE 08/06/2022: fixed a bug in which lastz would not align small fragmented genomes, as well as small contigs, in the source assembly. Anyone interested in these small contigs should discard the previous version of nf-LO using nextflow drop evotools/nf-LO, and repeat the analyses.

UPDATE 07/06/2022: Added the possibility of providing customized conservation scores in the q-format via the –qscores flag.

Quick start

Step-by-step example

Release notes

Notes