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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Derelle, Romain, Lees, John, Phelan, Jody, Lalvani, Ajit, Arinaminpathy, Nimalan, Chindelevitch, Leonid
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627351/
https://www.ncbi.nlm.nih.gov/pubmed/37871178
http://dx.doi.org/10.1093/bioinformatics/btad648
_version_ 1785131514902609920
author Derelle, Romain
Lees, John
Phelan, Jody
Lalvani, Ajit
Arinaminpathy, Nimalan
Chindelevitch, Leonid
author_facet Derelle, Romain
Lees, John
Phelan, Jody
Lalvani, Ajit
Arinaminpathy, Nimalan
Chindelevitch, Leonid
author_sort Derelle, Romain
collection PubMed
description 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.
format Online
Article
Text
id pubmed-10627351
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-106273512023-11-07 fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing Derelle, Romain Lees, John Phelan, Jody Lalvani, Ajit Arinaminpathy, Nimalan Chindelevitch, Leonid Bioinformatics Applications Note 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. Oxford University Press 2023-10-23 /pmc/articles/PMC10627351/ /pubmed/37871178 http://dx.doi.org/10.1093/bioinformatics/btad648 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Derelle, Romain
Lees, John
Phelan, Jody
Lalvani, Ajit
Arinaminpathy, Nimalan
Chindelevitch, Leonid
fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
title fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
title_full fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
title_fullStr fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
title_full_unstemmed fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
title_short fastlin: an ultra-fast program for Mycobacterium tuberculosis complex lineage typing
title_sort fastlin: an ultra-fast program for mycobacterium tuberculosis complex lineage typing
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627351/
https://www.ncbi.nlm.nih.gov/pubmed/37871178
http://dx.doi.org/10.1093/bioinformatics/btad648
work_keys_str_mv AT derelleromain fastlinanultrafastprogramformycobacteriumtuberculosiscomplexlineagetyping
AT leesjohn fastlinanultrafastprogramformycobacteriumtuberculosiscomplexlineagetyping
AT phelanjody fastlinanultrafastprogramformycobacteriumtuberculosiscomplexlineagetyping
AT lalvaniajit fastlinanultrafastprogramformycobacteriumtuberculosiscomplexlineagetyping
AT arinaminpathynimalan fastlinanultrafastprogramformycobacteriumtuberculosiscomplexlineagetyping
AT chindelevitchleonid fastlinanultrafastprogramformycobacteriumtuberculosiscomplexlineagetyping

Ejemplares similares