A survey of mapping algorithms in the long-reads era.
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
01 06 2023
01 06 2023
Historique:
received:
03
08
2022
accepted:
12
05
2023
medline:
5
6
2023
pubmed:
2
6
2023
entrez:
1
6
2023
Statut:
epublish
Résumé
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend framework used for short reads to a seed-and-chain framework due to the seed abundance in each read. The main novelties are based on alternative seed constructs or chaining formulations. Dozens of tools now exist, whose heuristics have evolved considerably. We provide an overview of the methods used in long-read mappers. Since they are driven by implementation-specific parameters, we develop an original visualization tool to understand the parameter settings ( http://bcazaux.polytech-lille.net/Minimap2/ ).
Identifiants
pubmed: 37264447
doi: 10.1186/s13059-023-02972-3
pii: 10.1186/s13059-023-02972-3
pmc: PMC10236595
doi:
Types de publication
Journal Article
Review
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
133Informations de copyright
© 2023. The Author(s).
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