Bioinformatics tools and databases for analysis of next-generation sequence data

Comparative studies of de novo assembly tools for next-generation sequencing technologies

(2011) Yong Lin et al.   BIOINFORMATICS

Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format

(2011) M. N. Edmonson et al.   BIOINFORMATICS

SHRiMP2: Sensitive yet Practical Short Read Mapping

(2011) Matei David et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Multiplexed microsatellite recovery using massively parallel sequencing

(2011) T. N. JENNINGS et al.   Molecular Ecology Resources

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS

(2011) Paul J. Berkman et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2011) Wenyu Zhang et al.   PLoS One

Savant: genome browser for high-throughput sequencing data

(2010) M. Fiume et al.   BIOINFORMATICS

PE-Assembler: de novo assembler using short paired-end reads

(2010) Pramila Nuwantha Ariyaratne et al.   BIOINFORMATICS

Future tools for association mapping in crop plantsThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Chris Duran et al.   GENOME

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

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

(2010) H. Hou et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Targeted identification of genomic regions using TAGdb

(2010) Daniel J Marshall et al.   Plant Methods

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

Genome sequence data: management, storage, and visualization

(2009) Jacqueline Batley et al.   BIOTECHNIQUES

Microsatellite discovery by deep sequencing of enriched genomic libraries

(2009) Quentin C. Santana et al.   BIOTECHNIQUES

Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing

(2009) Jawad Abdelkrim et al.   BIOTECHNIQUES

De novo sequencing of plant genomes using second-generation technologies

(2009) M. Imelfort et al.   BRIEFINGS IN BIOINFORMATICS

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

(2009) D. S. Horner et al.   BRIEFINGS IN BIOINFORMATICS

Molecular Genetic Markers: Discovery, Applications, Data Storage and Visualisation

(2009) Chris Duran et al.   Current Bioinformatics

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

Single nucleotide polymorphism discovery in barley using autoSNPdb

(2009) Chris Duran et al.   PLANT BIOTECHNOLOGY JOURNAL

Discovering genetic polymorphisms in next-generation sequencing data

(2009) Michael Imelfort et al.   PLANT BIOTECHNOLOGY JOURNAL

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

(2009) Daniel R. Zerbino et al.   PLoS One

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

SHRiMP: Accurate Mapping of Short Color-space Reads

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

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

(2009) Iain MacCallum et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

SeqAn An efficient, generic C++ library for sequence analysis

(2008) Andreas Döring et al.   BMC BIOINFORMATICS

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Quality scores and SNP detection in sequencing-by-synthesis systems

(2008) W. Brockman 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

De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer

(2008) D. Hernandez et al.   GENOME RESEARCH

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

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

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS

AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants

(2008) C. Duran et al.   NUCLEIC ACIDS RESEARCH

Short read fragment assembly of bacterial genomes

(2007) M. J. Chaisson et al.   GENOME RESEARCH