Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algo - Archive ouverte HAL Accéder directement au contenu
Pré-Publication, Document De Travail Année : 2023

Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algo

Résumé

The diversity of the immune repertoire is grounded on V(D)J recombinations in several loci. Many algorithms and software detect and designate these recombinations in high-throughput sequencing data. To improve their efficiency, we propose a multi-loci seed identification through an Aho-Corasick like automaton as well as a seed-based gene filtration. These algorithms were implemented into Vidjil-algo, used routinely by several labs for the analysis of hematologic malignancies. We benchmark the results of Vidjil-algo and of MiXCR on five datasets, evaluating the specificity and sensitivity of the detection, as well as the adequation of the designation to manually curated sequences. Compared to the previous algorithms, the new algorithms implemented in Vidjil-algo bring speedups between 5x and 30x, with a smaller memory footprint and without quality loss in results. They enable to precisely annotate in a few minutes millions of sequences coming from V(D)J recombinations, including incomplete V(D)J-like recombinations, improving our knowledge on immune repertoires.
Fichier principal
Vignette du fichier
vidjil-algo.pdf (404.56 Ko) Télécharger le fichier
vidjil-algo-supp.pdf (137.14 Ko) Télécharger le fichier
Origine : Fichiers produits par l'(les) auteur(s)

Dates et versions

hal-04361907 , version 1 (22-12-2023)

Identifiants

  • HAL Id : hal-04361907 , version 1

Citer

Cyprien Borée, Mathieu Giraud, Mikaël Salson. Alignment-free detection and seed-based identification of multi-loci V(D)J recombinations in Vidjil-algo. 2023. ⟨hal-04361907⟩
73 Consultations
42 Téléchargements

Partager

Gmail Facebook X LinkedIn More