Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects

Parameters for accurate genome alignment

(2012) Martin C Frith et al.   BMC BIOINFORMATICS

Exome sequencing and the genetic basis of complex traits

(2012) Adam Kiezun et al.   NATURE GENETICS

Quake: quality-aware detection and correction of sequencing errors

(2012) David R Kelley et al.   GENOME BIOLOGY

Comparative analysis of algorithms for next-generation sequencing read alignment

(2011) M. Ruffalo et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage

(2011) R. A. Farrer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Correction of sequencing errors in a mixed set of reads

(2010) L. Salmela   BIOINFORMATICS

Filtering error from SOLiD Output

(2010) Ariella Sasson et al.   BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

EDAR: An Efficient Error Detection and Removal Algorithm for Next Generation Sequencing Data

(2010) Xiaohong Zhao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Single nucleotide differences (SNDs) in the dbSNP database may lead to errors in genotyping and haplotyping studies

(2009) Lucia Musumeci et al.   HUMAN MUTATION

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

SHRiMP: Accurate Mapping of Short Color-space Reads

(2009) Stephen M. Rumble et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

ZOOM! Zillions of oligos mapped

(2008) H. Lin et al.   BIOINFORMATICS

De novoassembly of thePseudomonas syringaepv.syringaeB728a genome using Illumina/Solexa short sequence reads

(2008) Rhys A. Farrer et al.   FEMS MICROBIOLOGY LETTERS

Characterization of pairwise and multiple sequence alignment errors

(2008) Giddy Landan et al.   GENE

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

(2008) H. Li et al.   GENOME RESEARCH