Identifies LTR retrotransposons using LTR_retriever
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:'sample1' ]
[ id:'sample1' ]
genome{:bash}
:file
Genomic sequences in fasta format
*.{fsa,fa,fasta}
harvest{:bash}
LTR-RT candidates from GenomeTools ltrharvest in the old tabular format
*.tabout
finder{:bash}
LTR-RT candidates from LTR_FINDER
*.scn
mgescan{:bash}
LTR-RT candidates from MGEScan_LTR
*.out
non_tgca{:bash}
Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format
log{:bash}
*.log{:bash}
Output log from LTR_retriever
*.log
pass_list{:bash}
${prefix}.pass.list{:bash}
Intact LTR-RTs with coordinate and structural information in summary table format
*.pass.list
pass_list_gff{:bash}
*.pass.list.gff3{:bash}
Intact LTR-RTs with coordinate and structural information in gff3 format
*.pass.list.gff3
ltrlib{:bash}
*.LTRlib.fa{:bash}
All non-redundant LTR-RTs
*.LTRlib.fa
annotation_out{:bash}
${prefix}.out{:bash}
Whole-genome LTR-RT annotation by the non-redundant library
annotation_gff{:bash}
*.out.gff3{:bash}
Whole-genome LTR-RT annotation by the non-redundant library in gff3 format
*.out.gff3
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Sensitive and accurate identification of LTR retrotransposons
