fastlin: an ultra-fast program for <i>Mycobacterium tuberculosis</i> complex lineage typing-Reference-Cited by-同舟云学术

fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing

Published:2023-10-23 Issue:11 Volume:39 Page:
ISSN:1367-4811
Container-title:Bioinformatics
language:en
Short-container-title:

Author:

Derelle Romain¹^ORCID,Lees John²³^ORCID,Phelan Jody⁴^ORCID,Lalvani Ajit¹,Arinaminpathy Nimalan¹²,Chindelevitch Leonid²^ORCID

Affiliation:

1. NIHR Health Protection Research Unit in Respiratory Infections, National Heart and Lung Institute, Imperial College London , London W2 1PG, United Kingdom

2. MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London , London W12 0BZ, United Kingdom

3. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus , Hinxton CB10 1SD, United Kingdom

4. Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine , London WC1E 7HT, United Kingdom

Abstract

Abstract Summary Fastlin is a bioinformatics tool designed for rapid Mycobacterium tuberculosis complex (MTBC) lineage typing. It utilizes an ultra-fast alignment-free approach to detect previously identified barcode single nucleotide polymorphisms associated with specific MTBC lineages. In a comprehensive benchmarking against existing tools, fastlin demonstrated high accuracy and significantly faster running times. Availability and implementation fastlin is freely available at https://github.com/rderelle/fastlin and can easily be installed using Conda.

Funder

NIHR Health Protection Research Unit

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

Link

https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad648/52417556/btad648.pdf

Reference15 articles.

1. QuantTB—a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data;Anyansi;BMC Genomics,2020

2. Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study;Bryant;Lancet Respir Med,2013

3. Development and application of affordable SNP typing approaches to genotype Mycobacterium tuberculosis complex strains in low and high burden countries;Cancino-Muñoz;Sci Rep,2019

4. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains;Coll;Nat Commun,2014

5. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history;Coscolla;Microb Genom,2021

Cited by 4 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. TBtypeR: Sensitive detection and sublineage classification of low-frequencyMycobacterium tuberculosiscomplex mixed infections;2024-06-13

2. Tuberculosis research: Quo vadis;Drug Target Insights;2024-05-31

3. Demixer: A probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample;2024-04-15

4. Seamless, rapid and accurate analyses of outbreak genomic data using Split K-mer Analysis (SKA);2024-03-29