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 05/2024: The --aligner minimap2 mode now runs in multiple processes, splitting the target genome in fragments of at least --tgtSize bases; individual contigs and scaffolds will not be fragmented, and each chunk will contain entire sequences, unless the --mm2_lowmem option is provided. The old approach is still accessible through the --mm2_full_alignment option. The anaconda recipe with the dependencies has been updated, so please ensure to re-create the container where needed. This optimization allows to liftover the panTro6 to the hg38 genomes on a 16-cores Ryzen 7 8700G, 64G Ubuntu machine in under half an hour.
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.
.. toctree:: :maxdepth: 1 :caption: Step-by-step example step
.. toctree:: :maxdepth: 1 :caption: Installation install customconf
.. toctree:: :maxdepth: 0 :caption: Components inputs resources alignments chain liftover output reports changelog citations
.. toctree:: :maxdepth: 0 :caption: Notes notes