Description

Generates an interactive HTML dashboard integrating taxonomy, annotation, and metadata to detect contamination in metagenomic and amplicon sequencing datasets. GRIMER is independent of quantification methods and directly analyses contingency tables.

Input

Name
Description
Pattern

0 ()

1 ()

sample_metadata (file)

Tab-separated metadata file. Rows are samples; columns are metadata fields. Optional, pass [] to omit.

*.tsv

config (file)

YAML configuration file defining external tool references, controls, and annotations. Optional, pass [] to omit.

*.{yml,yaml}

Output

Name
Description
Pattern

0 ()

0 ()

Tools

grimer Documentation

GRIMER performs automated contamination analysis and generates portable interactive dashboards from contingency tables, integrating taxonomy, annotation and metadata.

https://github.com/pirovc/grimerdoi: 10.1101/2021.06.22.449360License: MIT
Authors