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
LTR-RT candidates from GenomeTools ltrharvest in the old tabular format
*.tabout
finder
LTR-RT candidates from LTR_FINDER
*.scn
mgescan
LTR-RT candidates from MGEScan_LTR
*.out
non_tgca
Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format
log
*.log
Output log from LTR_retriever
pass_list
${prefix}.pass.list
Intact LTR-RTs with coordinate and structural information in summary table format
*.pass.list
pass_list_gff
*.pass.list.gff3
Intact LTR-RTs with coordinate and structural information in gff3 format
ltrlib
*.LTRlib.fa
All non-redundant LTR-RTs
annotation_out
${prefix}.out
Whole-genome LTR-RT annotation by the non-redundant library
annotation_gff
*.out.gff3
Whole-genome LTR-RT annotation by the non-redundant library in gff3 format
versions
versions.yml
File containing software versions
Sensitive and accurate identification of LTR retrotransposons
