BWA-mem is not the best aligner for ancient DNA short reads

Autor: Bastien Llamas, Adrien Oliva, Raymond Tobler, Yassine Souilmi

Xu and colleagues (Xu et al., 2021) recently suggested a new parameterisation of BWA-mem (Li, 2013) as an alternative to the current standard BWA-aln (Li and Durbin, 2009) to process ancient DNA sequencing data. The authors tested several combination

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::828e9d4b09f562b6a8888ce7cc3e2227
https://doi.org/10.1101/2021.08.02.454401

Accounting for ambiguity in ancestral sequence reconstruction

Autor: Laurent Brehelin, Olivier Gascuel, Adrien Oliva, Sylvain Pulicani, Stéphane Guindon, Vincent Lefort

Publikováno v: Bioinformatics
Bioinformatics, Oxford University Press (OUP), 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩
Bioinformatics, 2019, 35 (21), pp.4290-4297. ⟨10.1093/bioinformatics/btz249⟩

MotivationThe reconstruction of ancestral genetic sequences from the analysis of contemporaneous data is a powerful tool to improve our understanding of molecular evolution. Various statistical criteria defined in a phylogenetic framework can be used

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d6be3b9f8e69cd8aea634f31a18984a0
https://hal-pasteur.archives-ouvertes.fr/pasteur-02404399/file/ancestral_clean.pdf

Systematic benchmark of ancient DNA read mapping.

Autor: Oliva, Adrien¹ (AUTHOR), Tobler, Raymond¹ (AUTHOR), Cooper, Alan² (AUTHOR), Llamas, Bastien^1,3 (AUTHOR), Souilmi, Yassine^1,3 (AUTHOR) yassine.souilmi@adelaide.edu.au

Publikováno v: Briefings in Bioinformatics. Sep2021, Vol. 22 Issue 5, p1-12. 12p.