Quake: quality-aware detection and correction of sequencing errors

Correction of sequencing errors in a mixed set of reads

(2010) L. Salmela   BIOINFORMATICS

Reptile: representative tiling for short read error correction

(2010) X. Yang et al.   BIOINFORMATICS

Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction

(2010) Lance E Palmer et al.   BMC BIOINFORMATICS

Application of second-generation sequencing to cancer genomics

(2010) K. Robison   BRIEFINGS IN BIOINFORMATICS

A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on CUDA-Enabled Graphics Hardware

(2010) Haixiang Shi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction

(2010) Osvaldo Zagordi et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Cancer genomics identifies determinants of tumor biology

(2010) Elaine R Mardis   GENOME BIOLOGY

SHREC: a short-read error correction method

(2009) J. Schroder et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data

(2009) Héctor Corrada Bravo et al.   BIOMETRICS

Finding optimal threshold for correction error reads in DNA assembling

(2009) Francis YL Chin et al.   BMC BIOINFORMATICS

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

(2009) S.-M. Ahn et al.   GENOME RESEARCH

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing

(2009) W.-C. Kao et al.   GENOME RESEARCH

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing

(2009) W. Qu et al.   GENOME RESEARCH

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

A comprehensive catalogue of somatic mutations from a human cancer genome

(2009) Erin D. Pleasance et al.   NATURE

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Probabilistic base calling of Solexa sequencing data

(2008) Jacques Rougemont et al.   BMC BIOINFORMATICS

De novo fragment assembly with short mate-paired reads: Does the read length matter?

(2008) M. J. Chaisson et al.   GENOME RESEARCH

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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

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

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Alta-Cyclic: a self-optimizing base caller for next-generation sequencing

(2008) Yaniv Erlich et al.   NATURE METHODS

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH