Related references
Note: Only part of the references are listed.Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries
Matthew R. Olm et al.
MSYSTEMS (2020)
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines
Stephen J. Bush et al.
GIGASCIENCE (2020)
An open resource for accurately benchmarking small variant and reference calls
Justin M. Zook et al.
NATURE BIOTECHNOLOGY (2019)
Dashing: fast and accurate genomic distances with HyperLogLog
Daniel N. Baker et al.
GENOME BIOLOGY (2019)
geck: trio-based comparative benchmarking of variant calls
Peter Komar et al.
BIOINFORMATICS (2018)
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
BIOINFORMATICS (2018)
Clinical sequencing: From raw data to diagnosis with lifetime value
S. M. Caspar et al.
CLINICAL GENETICS (2018)
MUMmer4: A fast and versatile genome alignment system
Guillaume Marcais et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
Genes significantly associated with lineage II food isolates of Listeria monocytogenes
Cary Pirone-Davies et al.
BMC GENOMICS (2018)
A universal SNP and small-indel variant caller using deep neural networks
Ryan Poplin et al.
NATURE BIOTECHNOLOGY (2018)
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Chirag Jain et al.
NATURE COMMUNICATIONS (2018)
A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
Michael A. Eberle et al.
GENOME RESEARCH (2017)
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
Daniel R. Mende et al.
NUCLEIC ACIDS RESEARCH (2017)
Database Resources of the National Center for Biotechnology
Richa Agarwala et al.
NUCLEIC ACIDS RESEARCH (2017)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Sergey Koren et al.
GENOME RESEARCH (2017)
VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data
Heiko Mueller et al.
NUCLEIC ACIDS RESEARCH (2017)
The quantitative impact of read mapping to non-native reference genomes in comparative RNA-Seq studies
Adam Price et al.
PLOS ONE (2017)
Short Read Mapping: An Algorithmic Tour
Stefan Canzar et al.
PROCEEDINGS OF THE IEEE (2017)
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
Ryan R. Wick et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model
Ruibang Luo et al.
GIGASCIENCE (2017)
Evaluating alignment and variant-calling software for mutation identification in C. elegans by whole-genome sequencing
Harold E. Smith et al.
PLOS ONE (2017)
Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data
Sarah Sandmann et al.
SCIENTIFIC REPORTS (2017)
VCF-Explorer: filtering and analysing whole genome VCF files
Mete Akgun et al.
BIOINFORMATICS (2017)
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
Alexa B. R. McIntyre et al.
GENOME BIOLOGY (2017)
Simulome: a genome sequence and variant simulator
Adam Price et al.
BIOINFORMATICS (2017)
SNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?
Bhavna Hurgobin et al.
BIOLOGY-BASEL (2017)
Review of alignment and SNP calling algorithms for next-generation sequencing data
M. Mielczarek et al.
JOURNAL OF APPLIED GENETICS (2016)
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
Nuala A. O'Leary et al.
NUCLEIC ACIDS RESEARCH (2016)
Reclassification of Clostridium difficile as Clostridioides difficile (Hall and O'Toole 1935) Prevot 1938
Paul A. Lawson et al.
ANAEROBE (2016)
Higher classification sensitivity of short metagenomic reads with CLARK-S
Rachid Ounit et al.
BIOINFORMATICS (2016)
An analytical workflow for accurate variant discovery in highly divergent regions
Shulan Tian et al.
BMC GENOMICS (2016)
SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
Yongchao Liu et al.
BMC SYSTEMS BIOLOGY (2016)
Centrifuge: rapid and sensitive classification of metagenomic sequences
Daehwan Kim et al.
GENOME RESEARCH (2016)
Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis
Robyn S. Lee et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2016)
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
Sudhir Kumar et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Fast and sensitive taxonomic classification for metagenomics with Kaiju
Peter Menzel et al.
NATURE COMMUNICATIONS (2016)
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Justin M. Zook et al.
SCIENTIFIC DATA (2016)
An evaluation of the accuracy and speed of metagenome analysis tools
Stinus Lindgreen et al.
SCIENTIFIC REPORTS (2016)
Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov et al.
GENOME BIOLOGY (2016)
Alignment of Next-Generation Sequencing Reads
Knut Reinert et al.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS, VOL 16 (2015)
Roary: rapid large-scale prokaryote pan genome analysis
Andrew J. Page et al.
BIOINFORMATICS (2015)
Complete genome sequence of the Clostridium difficile laboratory strain 630Δerm reveals differences from strain 630, including translocation of the mobile element CTn5
Erika van Eijk et al.
BMC GENOMICS (2015)
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
Sergey Koren et al.
CURRENT OPINION IN MICROBIOLOGY (2015)
Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection
Angela J. Taylor et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2015)
SpeedSeq: ultra-fast personal genome analysis and interpretation
Colby Chiang et al.
NATURE METHODS (2015)
HISAT: a fast spliced aligner with low memory requirements
Daehwan Kim et al.
NATURE METHODS (2015)
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
Phelim Bradley et al.
NATURE COMMUNICATIONS (2015)
A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference
Adam Cornish et al.
BIOMED RESEARCH INTERNATIONAL (2015)
Best practices for evaluating single nucleotide variant calling methods for microbial genomics
Nathan D. Olson et al.
FRONTIERS IN GENETICS (2015)
Systematic comparison of variant calling pipelines using gold standard personal exome variants
Sohyun Hwang et al.
SCIENTIFIC REPORTS (2015)
An ensemble approach to accurately detect somatic mutations using SomaticSeq
Li Tai Fang et al.
GENOME BIOLOGY (2015)
Performance evaluation of indel calling tools using real short-read data
Mohammad Shabbir Hasan et al.
HUMAN GENOMICS (2015)
Toward better understanding of artifacts in variant calling from high-coverage samples
Heng Li
BIOINFORMATICS (2014)
Evaluation of variant identification methods for whole genome sequencing data in dairy cattle
Christine F. Baes et al.
BMC GENOMICS (2014)
Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads
Frederic Bertels et al.
MOLECULAR BIOLOGY AND EVOLUTION (2014)
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
Andy Rimmer et al.
NATURE GENETICS (2014)
CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
Yongchao Liu et al.
PLOS ONE (2014)
MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
Wan-Ping Lee et al.
PLOS ONE (2014)
Choice of Reference Sequence and Assembler for Alignment of Listeria monocytogenes Short-Read Sequence Data Greatly Influences Rates of Error in SNP Analyses
Arthur W. Pightling et al.
PLOS ONE (2014)
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker et al.
PLOS ONE (2014)
Kraken: ultrafast metagenomic sequence classification using exact alignments
Derrick E. Wood et al.
GENOME BIOLOGY (2014)
The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes
Todd J. Treangen et al.
GENOME BIOLOGY (2014)
NextGenMap: fast and accurate read mapping in highly polymorphic genomes
Fritz J. Sedlazeck et al.
BIOINFORMATICS (2013)
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study
Timothy M. Walker et al.
LANCET INFECTIOUS DISEASES (2013)
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden
Quan Long et al.
NATURE GENETICS (2013)
Kraken: A set of tools for quality control and analysis Of high-throughput sequence data
Matthew P. A. Davis et al.
METHODS (2013)
Diverse Sources of C. difficile Infection Identified on Whole-Genome Sequencing
David W. Eyre et al.
NEW ENGLAND JOURNAL OF MEDICINE (2013)
Fast and accurate read mapping with approximate seeds and multiple backtracking
Enrico Siragusa et al.
NUCLEIC ACIDS RESEARCH (2013)
Variant Callers for Next-Generation Sequencing Data: A Comparison Study
Xiangtao Liu et al.
PLOS ONE (2013)
Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects
Rhys A. Farrer et al.
SCIENTIFIC REPORTS (2013)
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
Jason O'Rawe et al.
GENOME MEDICINE (2013)
VarSifter: Visualizing and analyzing exome-scale sequence variation data on a desktop computer
Jamie K. Teer et al.
BIOINFORMATICS (2012)
Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs
Christopher T. Saunders et al.
BIOINFORMATICS (2012)
A beginners guide to SNP calling from high-throughput DNA-sequencing data
Andre Altmann et al.
HUMAN GENETICS (2012)
The GEM mapper: fast, accurate and versatile alignment by filtration
Santiago Marco-Sola et al.
NATURE METHODS (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
Andreas Wilm et al.
NUCLEIC ACIDS RESEARCH (2012)
Consensus Rules in Variant Detection from Next-Generation Sequencing Data
Peilin Jia et al.
PLOS ONE (2012)
Genomes in a bottle: creating standard reference materials for genomic variation - why, what and how?
Justin M Zook et al.
GENOME BIOLOGY (2012)
Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data
Qi Liu et al.
BMC GENOMICS (2012)
Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
Gerton Lunter et al.
GENOME RESEARCH (2011)
Field guide to next-generation DNA sequencers
Travis C. Glenn
MOLECULAR ECOLOGY RESOURCES (2011)
A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo et al.
NATURE GENETICS (2011)
APPLICATIONS OF NEXT-GENERATION SEQUENCING Genome structural variation discovery and genotyping
Can Alkan et al.
NATURE REVIEWS GENETICS (2011)
SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data
Zhi Wei et al.
NUCLEIC ACIDS RESEARCH (2011)
Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on the Origin of the Haitian Outbreak
Rene S. Hendriksen et al.
MBIO (2011)
Cliff's Delta Calculator: A non-parametric effect size program for two groups of observations
Guillermo Macbeth et al.
UNIVERSITAS PSYCHOLOGICA (2011)
GASSST: global alignment short sequence search tool
Guillaume Rizk et al.
BIOINFORMATICS (2010)
A survey of sequence alignment algorithms for next-generation sequencing
Heng Li et al.
BRIEFINGS IN BIOINFORMATICS (2010)
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna et al.
GENOME RESEARCH (2010)
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Daniel C. Koboldt et al.
BIOINFORMATICS (2009)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Evolution and Diversity of Clonal Bacteria: The Paradigm of Mycobacterium tuberculosis
Tiago Dos Vultos et al.
PLOS ONE (2008)
The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome
Mohammed Sebaihia et al.
NATURE GENETICS (2006)
Strain-specific differences in Neisseria gonorrhoeae associated with the phase variable gene repertoire -: art. no. 21
PW Jordan et al.
BMC MICROBIOLOGY (2005)
Escherichia coli in disguise:: molecular origins of Shigella
RT Lan et al.
MICROBES AND INFECTION (2002)
Correlations between molecular subtyping and serotyping of Listeria monocytogenes
CA Nadon et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2001)