scholarly journals Improving long-read accuracy

2018 ◽  
Vol 15 (11) ◽  
pp. 860-860
Author(s):  
Lei Tang
Keyword(s):  
Long Read ◽  
Read Accuracy

scholarly journals Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

2019 ◽  
Vol 36 (5) ◽  
pp. 1374-1381 ◽  
Author(s):  
Antoine Limasset ◽  
Jean-François Flot ◽  
Pierre Peterlongo
Keyword(s):  
Supplementary Information ◽  
De Bruijn Graph ◽  
Sequence Information ◽  
Short Read ◽  
De Bruijn Graphs ◽  
Short Reads ◽  
Sequencing Errors ◽  
Long Read ◽  
De Bruijn ◽  
Read Accuracy

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.

scholarly journals Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs

2019 ◽  
Author(s):  
Antoine Limasset ◽  
Jean-François Flot ◽  
Pierre Peterlongo
Keyword(s):  
Large Data ◽  
De Bruijn Graph ◽  
Data Sets ◽  
Short Read ◽  
De Bruijn Graphs ◽  
Short Reads ◽  
Sequencing Errors ◽  
Long Read ◽  
De Bruijn ◽  
Read Accuracy

AbstractMotivationsShort-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 data sets or consider reads as mere suites of k-mers, without taking into account their full-length read information.ResultsWe 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 ImplementationThe implementation is open source and available at http://github.com/Malfoy/BCOOL under the Affero GPL license and as a Bioconda package.ContactAntoine Limasset [email protected] & Jean-François Flot [email protected] & Pierre Peterlongo [email protected]

scholarly journals Improving PacBio Long Read Accuracy by Short Read Alignment

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e46679 ◽  
Author(s):  
Kin Fai Au ◽  
Jason G. Underwood ◽  
Lawrence Lee ◽  
Wing Hung Wong
Keyword(s):  
Short Read ◽  
Read Alignment ◽  
Short Read Alignment ◽  
Long Read ◽  
Read Accuracy

scholarly journals Analysis of HLA-G long-read genomic sequences in mother–offspring pairs with preeclampsia

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ayako Nishizawa ◽  
Kazuki Kumada ◽  
Keiko Tateno ◽  
Maiko Wagata ◽  
Sakae Saito ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Polymorphisms ◽  
Genomic Dna ◽  
Genomic Sequences ◽  
Genomic Sequencing ◽  
Public Database ◽  
Coding Sequences ◽  
Pacbio Rs Ii ◽  
Potential Association ◽  
Long Read

AbstractPreeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.

scholarly journals Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders

2021 ◽  
Vol 2 (2) ◽  
pp. 100023
Author(s):  
Susan M. Hiatt ◽  
James M.J. Lawlor ◽  
Lori H. Handley ◽  
Ryne C. Ramaker ◽  
Brianne B. Rogers ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Molecular Diagnosis ◽  
Neurodevelopmental Disorders ◽  
Long Read
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