GFF3-LTR-Mapper

GFF3-LTR-Mapper is a command-line workflow for auditing and summarising EDTA intact LTR GFF3 annotations. This release focuses on scientist-facing, TSV-first analysis of intact LTR retrotransposon calls. The software validates intact-element structure, preserves QC traceability for every EDTA repeat_region, and produces simplified outputs for genome-scale, scaffold-scale, and coordinate-window comparisons. It also supports batch processing of many EDTA GFF3 files for cross-sample and cross-species comparisons. Key capabilities in this release include: - strict QC validation of EDTA intact LTR annotations - simplified scientist_regions.tsv and scientist_elements.tsv outputs - batch summaries across many samples - coordinate-window comparisons such as --region 1-3000000 - window-normalized metrics including intact elements per Mb and window coverage - support for .gff3 and .gff3.gz inputs - ASCII-only postcard output for optional lightweight visualization This software is intended for EDTA intact-element GFF3 output only. Summaries are restricted to intact LTR elements. Cross-species region comparisons in this release are coordinate-window comparisons and are not synteny-aware or homology-aware locus comparisons. The archive includes the Python source distribution, wheel distribution, citation metadata, and documentation/example materials for reproducible use.