Curated Metagenomics Sequencing Processing Coordinator
This repository contains:
- The pipeline itself
- A web-based coordinator and API
- Infrastructure tooling such as scripts and dockerfiles
Included software and tooling
The pipeline
The pipeline is a single-sample workflow written in Nextflow.
Software used in the pipeline
- humann2
- bowtie2
- diamond
- biopython
- biom-format
- metaphlan2
API
Written in python, uses fastapi. Postgresql backend.