Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database

(2016) James J. Davis et al.   Frontiers in Microbiology

Antimicrobial Resistance Prediction in PATRIC and RAST

(2016) James J. Davis et al.   Scientific Reports

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research

(2015) Andrew S. Warren et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Curation, integration and visualization of bacterial virulence factors in PATRIC

(2014) Chunhong Mao et al.   BIOINFORMATICS

Type material in the NCBI Taxonomy Database

(2014) Scott Federhen   NUCLEIC ACIDS RESEARCH

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

(2014) Wan-Ping Lee et al.   PLoS One

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

(2013) Scott C. Clark et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

The complex transcriptional landscape of the anucleate human platelet

(2013) Paul F Bray et al.   BMC GENOMICS

DrugBank 4.0: shedding new light on drug metabolism

(2013) Vivian Law et al.   NUCLEIC ACIDS RESEARCH

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Computational analysis of bacterial RNA-Seq data

(2013) Ryan McClure et al.   NUCLEIC ACIDS RESEARCH

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam et al.   NUCLEIC ACIDS RESEARCH

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

De novo genome assembly: what every biologist should know

(2012) Monya Baker   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

Incorporating sequence quality data into alignment improves DNA read mapping

(2010) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH

The European Nucleotide Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

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

FIGfams: yet another set of protein families

(2009) Folker Meyer et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genome-wide analysis of the interaction between the endosymbiotic bacterium Wolbachia and its Drosophila host

(2008) Zhiyong Xi et al.   BMC GENOMICS

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

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

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH