Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.
Bioinformatics
; 36(5): 1374-1381, 2020 03 01.
Article
de En
| MEDLINE
| ID: mdl-30785192
ABSTRACT
MOTIVATION Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence information. RESULTS:
We propose a new method to correct short reads using de Bruijn graphs and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads than k-mer-spectrum correctors while being scalable to human-size genomic datasets and beyond. AVAILABILITY AND IMPLEMENTATION The implementation is open source, available at http//github.com/Malfoy/BCOOL under the Affero GPL license and as a Bioconda package. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texte intégral:
1
Collection:
01-internacional
Base de données:
MEDLINE
Sujet principal:
Algorithmes
/
Séquençage nucléotidique à haut débit
Limites:
Humans
Langue:
En
Journal:
Bioinformatics
Sujet du journal:
INFORMATICA MEDICA
Année:
2020
Type de document:
Article
Pays d'affiliation:
Belgique