modules/ltrfinder

Finds full-length LTR retrotranspsons in genome sequences using the parallel version of LTR_Finder

genomicsannotationparallelrepeatlong terminal retrotransposonretrotransposon

https://github.com/nf-core/modules/[...]/modules/nf-core/ltrfinder

Description

Finds full-length LTR retrotranspsons in genome sequences using the parallel version of LTR_Finder

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`fasta`
`:file`

Genome sequences in fasta format

*.{fsa,fa,fasta}

Output

name:type

description

pattern

`scn`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.scn`
`:file`

Annotation in LTRharvest or LTR_FINDER format

*.scn

`gff`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.gff3`
`:file`

Annotation in gff3 format

*.gff3

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

LTR_FINDER_parallel
MIT

A Perl wrapper for LTR_FINDER

github.com/oushujun/LTR_FINDER_parallel 10.1186/s13100-019-0193-0

LTR_Finder
MIT

An efficient program for finding full-length LTR retrotranspsons in genome sequences

github.com/xzhub/LTR_Finder 10.1093/nar/gkm286

modules/ltrfinder

Description

Input

`meta`
`:map`

`fasta`
`:file`

Output

`scn`

`meta`
`:map`

`*.scn`
`:file`

`gff`

`meta`
`:map`

`*.gff3`
`:file`

`versions`

`versions.yml`
`:file`

Tools

LTR_FINDER_parallel
MIT

LTR_Finder
MIT

maintainer

get in touch

modules/ltrfinder

Description

Input

meta:map

fasta:file

Output

scn

meta:map

*.scn:file

gff

meta:map

*.gff3:file

versions

versions.yml:file

Tools

LTR_FINDER_parallel MIT

LTR_Finder MIT

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`scn`

`meta`
`:map`

`*.scn`
`:file`

`gff`

`meta`
`:map`

`*.gff3`
`:file`

`versions`

`versions.yml`
`:file`

LTR_FINDER_parallel
MIT

LTR_Finder
MIT