NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

(2014) Frederic Bertels et al.   MOLECULAR BIOLOGY AND EVOLUTION

Feeding the future

(2013) Susan McCouch et al.   NATURE

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes

(2013) Shea N. Gardner et al.   PLoS One

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

Current state-of-art of sequencing technologies for plant genomics research

(2012) M. Thudi et al.   Briefings in Functional Genomics

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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