RT Journal Article
SR Electronic
T1 Hostile: accurate host decontamination of microbial sequences
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.07.04.547735
DO 10.1101/2023.07.04.547735
A1 Constantinides, Bede
A1 Hunt, Martin
A1 Crook, Derrick W
YR 2023
UL http://biorxiv.org/content/early/2023/07/21/2023.07.04.547735.abstract
AB Motivation Microbial sequences generated from clinical samples are often contaminated with human host sequences that must be removed for ethical and legal reasons. Care must be taken to excise host sequences without inadvertently removing target microbial sequences to the detriment of downstream analyses such as variant calling and de novo assembly.Results To facilitate accurate host decontamination of both short and long sequencing reads, we developed Hostile, a tool capable of accurate host read removal using a laptop. We demonstrate that our approach removes at least 99.6% of real human reads and retains at least 99.989% of simulated bacterial reads. Using Hostile with a masked reference genome further increases bacterial read retention (>=99.997%) with negligible (<=0.001%) reduction in human read removal performance. Compared with an existing tool, Hostile removes 21-23% more human short reads and 22-43x fewer bacterial reads with comparable execution time.Availability and implementation Hostile is implemented as an MIT licensed Python package available from https://github.com/bede/hostile together with supplementary material.Competing Interest StatementThe authors have declared no competing interest.