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[MRG] fix kreport documentation #2302

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Sep 28, 2022
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[MRG] fix kreport documentation #2302

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6c67ea3
fix kreport doc
bluegenes Sep 28, 2022
4bb5166
formatting
bluegenes Sep 28, 2022
3c5fe99
be clearer about blank cols
bluegenes Sep 28, 2022
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55 changes: 35 additions & 20 deletions doc/command-line.md
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Original file line number Diff line number Diff line change
Expand Up @@ -648,31 +648,46 @@ Example reads-based `kreport` with all columns:
0.03 790 790 S 1747 Cutibacterium acnes
```

current sourmash `kreport` caveats:
- `Percent Reads [k-mers] Contained in Taxon`: weighted by k-mer abundance
- `Number of Reads [bp from k-mers] Contained in Taxon`: NOT WEIGHTED BY ABUNDANCE
sourmash `kreport` columns:
- `Percent [k-mers] contained in taxon` (abundance-weighted)
- `Estimated base pairs contained in taxon` (abundance-weighted)
- [blank column]
- `Rank Code`: (U)nclassified, (R)oot, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies.
- [blank column]
- `Scientific Name`: The scientific name of the taxon.

notes:
- `Number of Reads Assigned to Taxon` and `NCBI Taxon ID` will not be reported (blank entries).
- Rows are ordered by rank and then percent containment.
- Rows are ordered by rank and then ~percent containment.
- Since `gather` results are non-overlapping and all assignments are done at the
genome level, the percent match (first column) will sum to 100% at each rank
(aside from rounding issues) when including the unclassified (U) percentage.
Higher-rank assignments are generated using LCA-style summarization of genome
matches.

example sourmash `{output-name}.kreport.txt`:

```
0.13 1024000 D d__Bacteria
0.87 3990000 U unclassified
0.07 582000 P p__Bacteroidota
0.06 442000 P p__Proteobacteria
0.07 582000 C c__Bacteroidia
0.06 442000 C c__Gammaproteobacteria
0.07 582000 O o__Bacteroidales
0.06 442000 O o__Enterobacterales
0.07 582000 F f__Bacteroidaceae
0.06 442000 F f__Enterobacteriaceae
0.06 444000 G g__Prevotella
0.06 442000 G g__Escherichia
0.02 138000 G g__Phocaeicola
0.06 444000 S s__Prevotella copri
0.06 442000 S s__Escherichia coli
0.02 138000 S s__Phocaeicola vulgatus
0.95 2275774000 D Bacteria
0.01 28766999 D Eukaryota
0.03 82866000 U unclassified
0.77 1841829000 P Proteobacteria
0.18 433945000 P Firmicutes
0.01 19243000 P Ascomycota
.
.
.
0.47 1123782000 S Escherichia coli
0.01 17110000 S Saccharomyces cerevisiae
0.24 571653000 S Salmonella enterica
0.03 64374000 S Bacillus subtilis
0.02 38944000 S Listeria monocytogenes
0.04 104660000 S Staphylococcus aureus
0.06 145756000 S Limosilactobacillus fermentum
0.06 146394000 S Pseudomonas aeruginosa
0.03 80068000 S Enterococcus faecalis
0.00 2133000 S Saccharomyces pastorianus
0.00 143000 S Bacillus sp. KbaB1
```


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