ani_summary.tsv

ANI and alignment fraction (AF) between the user genomes and the GTDB species representative genomes, computed with skani. Tab-separated with the following columns:

  • user_genome: identifier of the query genome.

  • reference_genome: accession of the GTDB species representative genome.

  • skani_ani: ANI between the query and the reference genome.

  • skani_af: AF between the query and the reference genome (the larger of the query and reference alignment fractions reported by skani).

  • reference_taxonomy: GTDB taxonomy of the reference genome.

  • other_related_references(genome_id,species_name,radius,ANI,AF): classify_wf only, see summary.tsv.

Two versions of this file are written:

  • ani_rep writes <prefix>.ani_summary.tsv with one row for every skani hit of every query genome (sorted by decreasing AF, then ANI).

  • classify_wf writes classify/ani_screen/<prefix>.<domain>.ani_summary.tsv with one row per genome assigned to a species by the ANI screen (the representative it was assigned to), plus the other_related_references column. It is only written if at least one genome was assigned.

Produced by

Example

user_genome reference_genome        skani_ani       skani_af        reference_taxonomy
genome_1    GCF_000024185.1 100.0   1.0     d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium
genome_1    GCA_900321995.1 80.9    0.7     d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter sp900321995
genome_1    GCF_900114585.1 79.96   0.55    d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter olleyae
genome_2    GCA_002498365.1 99.16   0.94    d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002498365
genome_2    GCA_002505345.1 89.92   0.89    d__Archaea;p__Thermoplasmatota;c__Thermoplasmata;o__Methanomassiliicoccales;f__Methanomethylophilaceae;g__VadinCA11;s__VadinCA11 sp002505345