Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

Genome sequences in fasta format

*.{fsa,fa,fasta}

Output

name:type
description
pattern

scn{:bash}

meta{:bash}

:map

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

*.scn{:bash}

:file

Annotation in LTRharvest or LTR_FINDER format

*.scn

gff{:bash}

meta{:bash}

:map

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

*.gff3{:bash}

:file

Annotation in gff3 format

*.gff3

versions{:bash}

versions.yml{:bash}

: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
maintainer
Github user GallVp
get in touch
Ask a question on Slack Open an issue on GitHub