KrakenUniq¶
KrakenUniq is a novel metagenomics classifier that combines the fast k-mer-based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset.
Profile Format¶
Taxpasta expects a 9 column table. This file is generated with the KrakenUniq parameter --output. The accepted format is:
| Column Header | Description |
|---|---|
| % | |
| reads1 | |
| taxReads | |
| kmers | |
| dup | |
| cov | |
| taxID | |
| rank | |
| taxName |
Example¶
# KrakenUniq v1.0.0 DATE:2022-11-03T07:44:13Z DB:customdb/ DB_SIZE:358660 WD:/tmp/tmprujvrgk2/krakenuniq
# CL:perl /mnt/archgen/users/james_fellows_yates/bin/miniconda3/envs/mamba/envs/krakenuniq/bin/krakenuniq --db customdb/ --threads 8 --output test1.krakenuniq.classified.txt --report-file test1.krakenuniq.report.txt test_1.fastq.gz
% reads taxReads kmers dup cov taxID rank taxName
100 100 0 7556 1.3 0.1268 1 no rank root
100 100 0 7556 1.3 0.1268 10239 superkingdom Viruses
100 100 0 7556 1.3 0.1268 2559587 clade Riboviria
100 100 0 7556 1.3 0.1268 2732396 kingdom Orthornavirae
100 100 0 7556 1.3 0.1268 2732408 phylum Pisuviricota
100 100 0 7556 1.3 0.1268 2732506 class Pisoniviricetes
100 100 0 7556 1.3 0.1268 76804 order Nidovirales
100 100 0 7556 1.3 0.1268 2499399 suborder Cornidovirineae
100 100 0 7556 1.3 0.1268 11118 family Coronaviridae
100 100 0 7556 1.3 0.1268 2501931 subfamily Orthocoronavirinae
100 100 0 7556 1.3 0.1268 694002 genus Betacoronavirus
100 100 0 7556 1.3 0.1268 2509511 subgenus Sarbecovirus
100 100 0 7556 1.3 0.1268 694009 species Severe acute respiratory syndrome-related coronavirus
100 100 100 7556 1.3 0.1268 2697049 no rank Severe acute respiratory syndrome coronavirus 2
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Value used in standardised profile output ↩