Description

Classifies metagenomic sequence data

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

reads (file)

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

db (directory)

Path to directory containing centrifuge database files

save_unaligned (boolean)

If true unmapped fastq files are saved

save_aligned (boolean)

If true mapped fastq files are saved

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

report (file)

File containing a classification summary

*.{report.txt}

results (file)

File containing classification results

*.{results.txt}

sam (file)

Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s

*.{sam,tab}

fastq_unmapped (file)

Unmapped fastq files

*.unmapped.fastq.gz

fastq_mapped (file)

Mapped fastq files

*.mapped.fastq.gz

versions (file)

File containing software versions

versions.yml
included in
taxprofiler
authors
Github user sofstam Github user jfy133 Github user sateeshperi
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

centrifuge
GPL v3

Centrifuge is a classifier for metagenomic sequences.

ccb.jhu.edu/software/centrifuge ccb.jhu.edu/software/centrifuge/manual 10.1101/gr.210641.116