Jabba: hybrid error correction for long sequencing reads

Karect: accurate correction of substitution, insertion and deletion errors for next-generation sequencing data

(2015) Amin Allam et al.   BIOINFORMATICS

A Long Fragment Aligner called ALFALFA

(2015) Michaël Vyverman et al.   BMC BIOINFORMATICS

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Blue: correcting sequencing errors using consensus and context

(2014) Paul Greenfield et al.   BIOINFORMATICS

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

(2014) Romain Blanc-Mathieu et al.   BMC GENOMICS

essaMEM: finding maximal exact matches using enhanced sparse suffix arrays

(2013) Michaël Vyverman et al.   BIOINFORMATICS

Long read alignment based on maximal exact match seeds

(2012) Yongchao Liu et al.   BIOINFORMATICS

PBSIM: PacBio reads simulator—toward accurate genome assembly

(2012) Yukiteru Ono et al.   BIOINFORMATICS

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

Correcting errors in short reads by multiple alignments

(2011) L. Salmela et al.   BIOINFORMATICS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

SHREC: a short-read error correction method

(2009) J. Schroder et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH