Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads

(2014) Yun Heo et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

BayesHammer: Bayesian clustering for error correction in single-cell sequencing

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Probabilistic error correction for RNA sequencing

(2013) Hai-Son Le et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data

(2012) Yongchao Liu et al.   BIOINFORMATICS

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

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

Sim4db and Leaff: utilities for fast batch spliced alignment and sequence indexing

(2011) Brian Walenz et al.   BIOINFORMATICS

Correcting errors in short reads by multiple alignments

(2011) L. Salmela et al.   BIOINFORMATICS

Error correction of high-throughput sequencing datasets with non-uniform coverage

(2011) P. Medvedev et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly

(2011) Wei Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

HiTEC: accurate error correction in high-throughput sequencing data

(2010) L. Ilie et al.   BIOINFORMATICS

Correction of sequencing errors in a mixed set of reads

(2010) L. Salmela   BIOINFORMATICS

SHREC: a short-read error correction method

(2009) J. Schroder et al.   BIOINFORMATICS

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS