Description

Classifies metagenomic sequence data using unique k-mer counts

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

sequence_type (string)

Format of all given sequencing files as literal string, either 'fasta' or 'fastq'.

{fasta,fastq}

db (directory)

KrakenUniq database

save_output_reads (boolean)

Optionally, commands are added to save classified and unclassified reads as FASTQ or FASTA files depending on the input format. When the input is paired-end, the single output FASTQ contains merged reads.

report_file (boolean)

Whether to generate a report of relative abundances.

save_output (boolean)

Whether to save a file reporting the taxonomic classification of each input read.

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

krakenuniq Documentation

Metagenomics classifier with unique k-mer counting for more specific results

doi: 10.1186/s13059-018-1568-0License: MIT
Authors