Quadram Institute MetaBarcoding Analysis

A modular bioinformatics toolkit designed to facilitate metabarcoding analyses, with a focus on amplicon processing and sequence data management.

Introduction

Qimba provides a collection of commands for handling common tasks in metabarcoding workflows, including:

• Sequence processing and quality control
• Format conversions

Qimba CLI

Commands are organized into functional groups (run qimba --help to list them all):

Sample Management

• make-mapping: Generate sample sheets from sequence files
• show-samples: Display sample information from mapping files

Sequence Processing

• merge: Merge paired-end reads
• derep: Dereplicate sequences while preserving abundance information

Format Conversions

• dada2-split: Convert DADA2 output format to FASTA and simplified TSV

File Operations

• check-tab: Validate TSV file structure

Utility Commands

• version: Display Qimba version information

Example usage:

# Create a sample sheet from a directory of fastq files
qimba make-mapping data_dir -o mapping.tsv

# Merge paired-end reads
qimba merge -i mapping.tsv -o merged.fastq --threads 8

# Dereplicate sequences
qimba derep -i merged.fasta -o unique.fasta

Configuration

Qimba uses a configuration file located at ~/.config/qimba.ini. Default settings:

[qimba]
default_output_dir = .
threads = 4

Override configuration using command-line options or by specifying a custom config file:

qimba --config my_config.ini [command]

Contributing

We welcome contributions! Please check our Developer Documentation for information about:

• Code structure
• Adding new commands
• Testing guidelines
• Best practices

See [https://www.contributor-covenant.org/](Contributor covenant)

Authors

Qimba is developed and maintained by Quadram Institute Bioscience - Core Bioinformatics.

License

MIT