Simple bacterial assembly and annotation pipeline
Branch: master
Clone or download
Pull request Compare This branch is even with andreas-wilm:master.
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.github
assets
bin
conf
docs
.gitattributes
.gitignore
.travis.yml
CHANGELOG.md
CODE_OF_CONDUCT.md
Dockerfile
LICENSE
README.md
Singularity
environment.yml
main.nf
nextflow.config

README.md

nf-core/bacass

Simple bacterial assembly and annotation pipeline

Build Status Nextflow

install with bioconda Docker Singularity Container available

Introduction

This pipeline is for bacterial assembly of next-gen sequencing reads. It quality-trims your reads, runs QC, including a metagenomics classifier on your reads to check for purity, assembles the reads with Unicycler, annotates the assembly with Prokka and runs Quast on the assembly for quality check.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

Documentation

The nf-core/bacass pipeline comes with documentation about the pipeline, found in the docs/ directory:

  1. Installation
  2. Pipeline configuration
  3. Running the pipeline
  4. Output and how to interpret the results
  5. Troubleshooting

Credits

nf-core/bacass was originally written by Andreas Wilm.