PEAR: a fast and accurate Illumina Paired-End reAd mergeR

COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly

(2012) B. Liu et al.   BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

(2011) Zhangying Wang et al.   BMC GENOMICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

BIPES, a cost-effective high-throughput method for assessing microbial diversity

(2010) Hong-Wei Zhou et al.   ISME Journal

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

(2010) Gregory B. Gloor et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY