Description

Identifies LTR retrotransposons using LTR_retriever

Input

Name
Description
Pattern

meta (map)

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

genome (file)

Genomic sequences in fasta format

*.{fsa,fa,fasta}

harvest (file)

LTR-RT candidates from GenomeTools ltrharvest in the old tabular format

*.tabout

finder (file)

LTR-RT candidates from LTR_FINDER

*.scn

mgescan (file)

LTR-RT candidates from MGEScan_LTR

*.out

non_tgca (file)

Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format

*.tabout

Output

Name
Description
Pattern

meta (map)

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

log (file)

Output log from LTR_retriever

*.log

pass_list (file)

Intact LTR-RTs with coordinate and structural information in summary table format

*.pass.list

pass_list_gff (file)

Intact LTR-RTs with coordinate and structural information in gff3 format

*.pass.list.gff3

ltrlib (file)

All non-redundant LTR-RTs

*.LTRlib.fa

annotation_out (file)

Whole-genome LTR-RT annotation by the non-redundant library

*.out

annotation_gff (file)

Whole-genome LTR-RT annotation by the non-redundant library in gff3 format

*.out.gff3

versions (file)

File containing software versions

versions.yml

Tools

LTR_retriever Documentation

Sensitive and accurate identification of LTR retrotransposons

doi: 10.1104/pp.17.01310License: GPL v3
Authors