A survey of mapping algorithms in the long-reads era

Sahlin, Kristoffer; Baudeau, Thomas; Cazaux, Bastien; Marchet, Camille

Document type :

Compte-rendu et recension critique d'ouvrage

DOI :

10.1186/s13059-023-02972-3

Title :

A survey of mapping algorithms in the long-reads era

Author(s) :

Sahlin, Kristoffer [Auteur]
Science for Life Laboratory [Solna]
Baudeau, Thomas [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Université de Lille
Cazaux, Bastien [Auteur]

Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
École polytechnique universitaire de Lille [Polytech Lille]
Marchet, Camille [Auteur]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Institut des sciences informatiques et de leurs interactions - CNRS Sciences informatiques [INS2I-CNRS]

Journal title :

Genome Biology

Pages :

133

Publisher :

BioMed Central

Publication date :

2023-12

ISSN :

1465-6906

English keyword(s) :

Alignment
Sequence mapping
DNA

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]

English abstract : [en]

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 ...
Show more >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/ ).Show less >

Language :

Anglais

Popular science :

Non

ANR Project :

Modélisation Structurale d'ARN Intégrant des Données de Séquençage

Collections :