Description

Uses Liftoff to accurately map annotations in GFF or GTF between assemblies of the same, or closely-related species

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test' ]

target_fa (file)

Target assembly in fasta format

*.{fsa,fa,fasta}

ref_fa (file)

Reference assembly in fasta format

*.{fsa,fa,fasta}

ref_annotation (file)

Reference assembly annotations in gtf or gff3 format

*.{gtf,gff3}

ref_db (file)

Name of feature database; if not specified, the -g argument must
be provided and a database will be built automatically

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test' ]

gff3 (file)

Lifted annotations for the target assembly in gff3 format

*.gff3

polished_gff3 (file)

Polished lifted annotations for the target assembly in gff3 format

*.polished.gff3

unmapped_txt (file)

List of unmapped reference annotations

*.unmapped.txt

versions (file)

File containing software versions

versions.yml
maintainer
Github user GallVp
get in touch
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Tools

liftoff
GPL v3 License

Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species

github.com/agshumate/Liftoff 10.1093/bioinformatics/bty191