Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2013) J. Zhang et al.   BIOINFORMATICS

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

(2013) Sergey I Nikolenko et al.   BMC GENOMICS

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

(2012) John Archer et al.   BMC BIOINFORMATICS

Estimation of sequencing error rates in short reads

(2012) Xin Victoria et al.   BMC BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes

(2012) M. Schirmer et al.   BRIEFINGS IN BIOINFORMATICS

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

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

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

(2009) Martin Kircher et al.   GENOME BIOLOGY

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

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