Identifies LTR retrotransposons using LTR_retriever
meta:map
Groovy Map containing sample information e.g. [ id:'sample1' ]
[ 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
log
*.log:file
Output log from LTR_retriever
*.log
pass_list
${prefix}.pass.list:file
Intact LTR-RTs with coordinate and structural information in summary table format
*.pass.list
pass_list_gff
*.pass.list.gff3:file
Intact LTR-RTs with coordinate and structural information in gff3 format
*.pass.list.gff3
ltrlib
*.LTRlib.fa:file
All non-redundant LTR-RTs
*.LTRlib.fa
annotation_out
${prefix}.out:file
Whole-genome LTR-RT annotation by the non-redundant library
annotation_gff
*.out.gff3:file
Whole-genome LTR-RT annotation by the non-redundant library in gff3 format
*.out.gff3
versions
versions.yml:file
File containing software versions
versions.yml
Sensitive and accurate identification of LTR retrotransposons
