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 (can be gzipped)

*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}

ref_fa

:file

Reference assembly in fasta format (can be gzipped)

*.{fa,fa.gz,fasta,fasta.gz,fas,fas.gz,fsa,fsa.gz}

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

gff3

meta

:map

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

${prefix}.gff3

:file

Lifted annotations for the target assembly in gff3 format

*.gff3

polished_gff3

meta

:map

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

*.polished.gff3

:file

Polished lifted annotations for the target assembly in gff3 format

*.polished.gff3

unmapped_txt

meta

:map

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

*.unmapped.txt

:file

List of unmapped reference annotations

*.unmapped.txt

versions

versions.yml

:file

File containing software versions

versions.yml

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
included in
bacassgenomeassembler
maintainer
Github user GallVp
get in touch
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