DRAM Output

This is a work in progress, but here is an updated list of output files for DRAM2 as of May 11, 2026:

ANNOTATE/

  • raw-annotations.tsv — Initial gene annotations

  • raw_rrna_scan.tsv — rRNA scan results

  • collected_rrnas.tsv — Filtered rRNAs

  • collected_trnas.tsv — Filtered tRNAs

Subdirectories:

  • HMM_SEARCH/ — HMM-based functional annotation results

  • MMSEQ2/ — Sequence similarity search results

  • PRODIGAL/ — Gene predictions

  • QUAST/ — Assembly quality metrics

  • RENAMED_GFFS/ — Standardized GFF files

  • RENAMED_HEADERS/ — Renamed FASTA headers

multiqc/

  • multiqc_report.html — Aggregated QC report (HTML)

  • multiqc_data/ — subdirectory containing tool information and multiqc log

pipeline_info/ - contains logs, pipeline parameters, and execution traces
SUMMARIZE/

  • metabolism_summary.xlsx — excel workbook showing counts per MAG of curated gene sets

  • genome_stats.tsv — Per-genome statistics

  • summarized_genomes.tsv — text file with same information as the metabolism summary sheet

  • traits.xlsx — Per-MAG Traits

VISUALIZE/

  • product.html - Interactive heatmaps — Trait-based visualizations