Banzai-NGS 0.0.5

Banzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool

The Banzai Microbial Genomics Pipeline is currently in closed beta. Please star or follow this repository to receive updates when it’s publicly available.

Installation

See Install.rst

About

Banzai is a Microbial Genomics Next Generation Sequencing (NGS) Pipeline Tool developed within Dr Scott Beatson’s Group at the University of Queensland.

Banzai inherits it’s name from the Banzai ‘Pipeline’ surf break.

Banzai aims to simplify the analysis of large NGS datasets. It has been specifically designed to distribute the workload over internal and external High Performance Computing (HPC) resources as well as locally available workstations.

Core Features

Banzai allows for:

• data validation/quality control of NGS reads,

• de novo assembly of NGS reads,

• mapping of NGS reads to reference genomes,

• ordering of the contigs or scaffolds from draft assemblies against reference genomes,

• phylogenomics tasks (whole genome alignment, SNP based, recombination detection)

• annotating draft assemblies,

• enrichment of the annotation of draft assemblies,

• performing common utility tasks like the creation of BLAST databases, file format conversion and more.

Banzai supports the NGS platforms that are perdominantly used in Microbial Genomics projects.

The platforms include:

• Illumina (single end (SE), paired end (PE) and mate paired (MP) reads),

• 454 (SE and PE reads),

• ABI SOLiD colorspace reads and

• Pacific Biosciences reads (under development)

Banzai is by default geared towards 100 bp Illumina Paired End reads.

Philosophy

Banzai (in most cases) does not provide new NGS algorithms, it harnesses the power of published and tested NGS tools. Simply, Banzai simplifies, automates and distributes computational workloads which is the typical bottleneck in analysis of large NGS datasets.

Developers

The following have contributed significantly to Banzai:

• Mitchell Stanton-Cook (lead developer)

• Elizabeth Skippington (development of phylogenomics section)

• Nico Petty (design & testing)

• Nouri Ben Zakour (design and testing)

• Scott Beatson (design)