Browse source code (Github)Download Virtual Machine [vdi, 16Gb]Download dependancies [tar, 700 Mb]Download documentation [PDF, 1.5Mb]

Citing BugBuilder

A preprint of a manuscript in prepration is available on BioArxiv. If you use BugBuilder in your work, please cite :

Abbott James. C. (2017) BugBuilder - An Automated Microbial Genome Assembly and Analysis Pipeline bioRxiv 148783; doi:

Supported Platforms

  • Illumina GAII, HiSeq, MiSeq
  • Roche 454
  • IonTorrent
  • PacBio
  • MinION

Automated Microbial Genome Analysis

BugBuilder is a pipeline for hands-free assembly and analysis of microbial genome sequences. It produces outputs suitable either for direct submission to sequence databases or for use in downstream finishing processes. It is configurable to work with most command-line assembly and scaffolding tools which are selectable at run-time, and supports all common sequence types used in microbial genome assembly.

BugBuilder outputs

The BugBuilder workflow incorporates sequence pre-processing (quality assessment, read trimming, downsampling), contig assembly, scaffold assembly, annotation and generation of visualisations. Following assembly, validation processes can attempt to identify sequence misassemblies to facilitate genome finishing efforts.

BugBuilder is intended to allow high-throughput automated analysis of microbial genome sequences, in addition to allow scientists without specialist knowledge to carry out assembly and annotation tasks.

The quickest way of getting started with BugBuilder is to download the preconfigured virtual machine - instructions on setting this up are available on the BugBuilder Virtual Machine page.