v2.1.0
The following references were removed from the Lentivirus reference set due to significant overlap with the GRCh38.p14 human reference genome (RefSeq accession GCF_000001405.40):
- Lentivirus-wg-3825
- Lentivirus-wg-5653
- Lentivirus-wg-6651
- Lentivirus-wg-7194
- Lentivirus-wg-7734
The script used to determine this can be found here. The full output from this script is shown below:
2026-06-24 16:23:27 [INFO] epitome_filter: ======================================================================
2026-06-24 16:23:27 [INFO] epitome_filter: epitome_filter v1.0
2026-06-24 16:23:27 [INFO] epitome_filter: ======================================================================
2026-06-24 16:23:27 [INFO] epitome_filter: Configuration:
2026-06-24 16:23:27 [INFO] epitome_filter: Inputs: 1 files
2026-06-24 16:23:27 [INFO] epitome_filter: Output: updated.jsonl.gz
2026-06-24 16:23:27 [INFO] epitome_filter: Target: GCF_000001405.40_GRCh38.p14_genomic.fna
2026-06-24 16:23:27 [INFO] epitome_filter: Preset: asm20
2026-06-24 16:23:27 [INFO] epitome_filter: Min coverage: 10.000
2026-06-24 16:23:27 [INFO] epitome_filter: Min identity: 80.000
2026-06-24 16:23:27 [INFO] epitome_filter: Threads: 4
2026-06-24 16:23:27 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:23:27 [INFO] root: Loaded JSONL file: Lentivirus-wg.consensus.jsonl.gz
2026-06-24 16:23:27 [INFO] epitome_filter: Loaded 8965 records from Lentivirus-wg.consensus.jsonl.gz
2026-06-24 16:23:27 [INFO] epitome_filter: Loaded: 8965 records (8965 with sequence)
2026-06-24 16:23:27 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:23:28 [INFO] epitome_filter: Wrote 8965 query sequences → query.fasta
2026-06-24 16:23:28 [INFO] epitome_filter: Running: minimap2 -c -x asm20 -t 4 ../GCF_000001405.40_GRCh38.p14_genomic.fna /tmp/epitome_filter_ru2kad2f/query.fasta
2026-06-24 16:24:44 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:24:44 [INFO] epitome_filter: Evaluated 11 aligned records; 5 flagged for removal
2026-06-24 16:24:44 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:25:48 [INFO] epitome_filter: Wrote 8960 kept records → updated.jsonl.gz
2026-06-24 16:25:48 [INFO] epitome_filter: ======================================================================
2026-06-24 16:25:48 [INFO] epitome_filter: Filter summary (>=10% coverage & >=80% identity)
2026-06-24 16:25:48 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:25:48 [INFO] epitome_filter: Input records : 8965
2026-06-24 16:25:48 [INFO] epitome_filter: with sequence : 8965
2026-06-24 16:25:48 [INFO] epitome_filter: without sequence : 0
2026-06-24 16:25:48 [INFO] epitome_filter: Aligned to a target : 11
2026-06-24 16:25:48 [INFO] epitome_filter: Removed : 5
2026-06-24 16:25:48 [INFO] epitome_filter: Kept : 8960
2026-06-24 16:25:48 [INFO] epitome_filter: below threshold : 6
2026-06-24 16:25:48 [INFO] epitome_filter: no alignment : 8954
2026-06-24 16:25:48 [INFO] epitome_filter: no sequence : 0
2026-06-24 16:25:48 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:25:48 [INFO] epitome_filter: Removed records:
2026-06-24 16:25:48 [INFO] epitome_filter: Lentivirus|wg|3825 → NC_000001.11 cov=88.29% id=99.46%
2026-06-24 16:25:48 [INFO] epitome_filter: Lentivirus|wg|5653 → NC_000010.11 cov=94.00% id=99.61%
2026-06-24 16:25:48 [INFO] epitome_filter: Lentivirus|wg|6651 → NC_000006.12 cov=70.02% id=99.92%
2026-06-24 16:25:48 [INFO] epitome_filter: Lentivirus|wg|7194 → NC_000019.10 cov=41.79% id=99.97%
2026-06-24 16:25:48 [INFO] epitome_filter: Lentivirus|wg|7734 → NC_000011.10 cov=39.70% id=99.97%
2026-06-24 16:25:48 [INFO] epitome_filter: ======================================================================