Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment

Xu et al. (2021) recently recommended a new parameterization of BWA‐mem as a superior alternative to the widely‐used BWA‐aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA‐mem parameterization recommended by Xu et al. with the best‐performing alignment methods determined in t...

Descripción completa

Detalles Bibliográficos
Autores principales: Oliva, Adrien, Tobler, Raymond, Llamas, Bastien, Souilmi, Yassine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Letter to the Editor
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8717315/
https://www.ncbi.nlm.nih.gov/pubmed/35003706
http://dx.doi.org/10.1002/ece3.8297
_version_ 1784624505561284608
author Oliva, Adrien
Tobler, Raymond
Llamas, Bastien
Souilmi, Yassine
author_facet Oliva, Adrien
Tobler, Raymond
Llamas, Bastien
Souilmi, Yassine
author_sort Oliva, Adrien
collection PubMed
description Xu et al. (2021) recently recommended a new parameterization of BWA‐mem as a superior alternative to the widely‐used BWA‐aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA‐mem parameterization recommended by Xu et al. with the best‐performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that BWA‐aln is still the gold‐standard for ancient DNA read alignment .[Image: see text]
format Online
Article
Text
id pubmed-8717315
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher John Wiley and Sons Inc.
record_format MEDLINE/PubMed
spelling pubmed-87173152022-01-06 Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment Oliva, Adrien Tobler, Raymond Llamas, Bastien Souilmi, Yassine Ecol Evol Letter to the Editor Xu et al. (2021) recently recommended a new parameterization of BWA‐mem as a superior alternative to the widely‐used BWA‐aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA‐mem parameterization recommended by Xu et al. with the best‐performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that BWA‐aln is still the gold‐standard for ancient DNA read alignment .[Image: see text] John Wiley and Sons Inc. 2021-12-17 /pmc/articles/PMC8717315/ /pubmed/35003706 http://dx.doi.org/10.1002/ece3.8297 Text en © 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Letter to the Editor
Oliva, Adrien
Tobler, Raymond
Llamas, Bastien
Souilmi, Yassine
Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
title Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
title_full Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
title_fullStr Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
title_full_unstemmed Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
title_short Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment
title_sort additional evaluations show that specific bwa‐aln settings still outperform bwa‐mem for ancient dna data alignment
topic Letter to the Editor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8717315/
https://www.ncbi.nlm.nih.gov/pubmed/35003706
http://dx.doi.org/10.1002/ece3.8297
work_keys_str_mv AT olivaadrien additionalevaluationsshowthatspecificbwaalnsettingsstilloutperformbwamemforancientdnadataalignment
AT toblerraymond additionalevaluationsshowthatspecificbwaalnsettingsstilloutperformbwamemforancientdnadataalignment
AT llamasbastien additionalevaluationsshowthatspecificbwaalnsettingsstilloutperformbwamemforancientdnadataalignment
AT souilmiyassine additionalevaluationsshowthatspecificbwaalnsettingsstilloutperformbwamemforancientdnadataalignment

Ejemplares similares