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{:bash}

:map

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

target_fa{:bash}

:file

Target assembly in fasta format (can be gzipped)

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

ref_fa{:bash}

:file

Reference assembly in fasta format (can be gzipped)

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

ref_annotation{:bash}

:file

Reference assembly annotations in gtf or gff3 format

*.{gtf,gff3}

ref_db{:bash}

: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{:bash}

meta{:bash}

:map

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

${prefix}.gff3{:bash}

:file

Lifted annotations for the target assembly in gff3 format

*.gff3

polished_gff3{:bash}

meta{:bash}

:map

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

*.polished.gff3{:bash}

:file

Polished lifted annotations for the target assembly in gff3 format

*.polished.gff3

unmapped_txt{:bash}

meta{:bash}

:map

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

*.unmapped.txt{:bash}

:file

List of unmapped reference annotations

*.unmapped.txt

versions_liftoff{:bash}

${task.process}{:bash}

:string

The name of the process

liftoff{:bash}

:string

The name of the tool

liftoff --version | sed "s/v//"{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

liftoff{:bash}

:string

The name of the tool

liftoff --version | sed "s/v//"{:bash}

:eval

The expression to obtain the version of the tool

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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