RT Journal Article
SR Electronic
T1 Tychus: a whole genome sequencing pipeline for assembly, annotation and phylogenetics of bacterial genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 283101
DO 10.1101/283101
A1 Christopher Dean
A1 Noelle Noyes
A1 Steven Lakin
A1 Pablo Rovira-Sanz
A1 Xiang Yang
A1 Keith Belk
A1 Paul S. Morley
A1 Rick Meinersmann
A1 Zaid Abdo
YR 2018
UL http://biorxiv.org/content/early/2018/03/16/283101.abstract
AB Summary Tychus is a tool that allows researchers to perform massively parallel whole genome sequence (WGS) analysis with the goal of producing a high confidence and comprehensive description of the bacterial genome. Key features of the Tychus pipeline include the assembly, annotation, alignment, variant discovery and phylogenetic inference of large numbers of WGS isolates in parallel using open-source bioinformatics tools and virtualization technology. All prerequisite tools and dependencies come packaged together in a single suite that can be easily downloaded and installed on Linux and Mac operating systems.Availability Tychus is freely available as an open-source package under the MIT license, and can be downloaded via GitHub (https://github.com/Abdo-Lab/Tychus).Contact zaid.abdo{at}colostate.edu