Abstract
Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this
major human pathogen. Spoligotypes can be predicted from short read genome sequencing
data; however, no methods exist for long read sequence data such as from Nanopore or
PacBio. We present a novel software package Galru, which can rapidly detect the
spoligotype of a Mycobacterium tuberculosis sample from as little as a single uncorrected
long read. It allows for near real-time spoligotyping from long read data as it is being
sequenced, giving rapid sample typing. We compare it to the existing state of the art
software and find it performs identically to the results obtained from short read sequencing
data. Galru is freely available from https://github.com/quadram-institute-bioscience/galru
under the GPLv3 open source licence
major human pathogen. Spoligotypes can be predicted from short read genome sequencing
data; however, no methods exist for long read sequence data such as from Nanopore or
PacBio. We present a novel software package Galru, which can rapidly detect the
spoligotype of a Mycobacterium tuberculosis sample from as little as a single uncorrected
long read. It allows for near real-time spoligotyping from long read data as it is being
sequenced, giving rapid sample typing. We compare it to the existing state of the art
software and find it performs identically to the results obtained from short read sequencing
data. Galru is freely available from https://github.com/quadram-institute-bioscience/galru
under the GPLv3 open source licence
| Original language | Undefined/Unknown |
|---|---|
| Journal | bioRxiv |
| Publication status | Published - 2020 |
