相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。New approaches for metagenome assembly with short reads
Martin Ayling et al.
BRIEFINGS IN BIOINFORMATICS (2020)
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
Pierre-Alain Chaumeil et al.
BIOINFORMATICS (2020)
DeepMAsED: evaluating the quality of metagenomic assemblies
Olga Mineeva et al.
BIOINFORMATICS (2020)
A complete domain-to-species taxonomy for Bacteria and Archaea
Donovan H. Parks et al.
NATURE BIOTECHNOLOGY (2020)
METAVIRALSPADES: assembly of viruses from metagenomic data
Dmitry Antipov et al.
BIOINFORMATICS (2020)
Insights into the dynamics between viruses and their hosts in a hot spring microbial mat
Jessica K. Jarett et al.
ISME JOURNAL (2020)
910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens
Aditya Bandla et al.
SCIENTIFIC DATA (2020)
Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Paul Saary et al.
GENOME BIOLOGY (2020)
A new genomic blueprint of the human gut microbiota
Alexandre Almeida et al.
NATURE (2019)
New insights from uncultivated genomes of the global human gut microbiome
Stephen Nayfach et al.
NATURE (2019)
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline
Javier Tamames et al.
FRONTIERS IN MICROBIOLOGY (2019)
pTrimmer: An efficient tool to trim primers of multiplex deep sequencing data
Xiaolong Zhang et al.
BMC BIOINFORMATICS (2019)
Metagenomic analysis of gut microbiota alteration in a mouse model exposed to mycotoxin deoxynivalenol
Jun-Jie Wang et al.
TOXICOLOGY AND APPLIED PHARMACOLOGY (2019)
Composite Metagenome-Assembled Genomes Reduce the Quality of Public Genome Repositories
Alon Shaiber et al.
MBIO (2019)
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
Dongwan D. Kang et al.
PEERJ (2019)
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
Robert D. Stewart et al.
NATURE BIOTECHNOLOGY (2019)
GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets
Matthew D. Czajkowski et al.
BIOINFORMATICS (2019)
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
Edoardo Pasolli et al.
CELL (2019)
Mash Screen: high-throughput sequence containment estimation for genome discovery
Brian D. Ondov et al.
GENOME BIOLOGY (2019)
Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes
Nathan D. Olson et al.
BRIEFINGS IN BIOINFORMATICS (2019)
Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT
F. A. Bastiaan von Meijenfeldt et al.
GENOME BIOLOGY (2019)
fastp: an ultra-fast all-in-one FASTQ preprocessor
Shifu Chen et al.
BIOINFORMATICS (2018)
Genome-reconstruction for eukaryotes from complex natural microbial communities
Patrick T. West et al.
GENOME RESEARCH (2018)
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level
Luis M. Rodriguez-R et al.
NUCLEIC ACIDS RESEARCH (2018)
Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants
Stefano Campanaro et al.
WATER RESEARCH (2018)
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
Robert D. Stewart et al.
NATURE COMMUNICATIONS (2018)
Metagenomic analysis of basal ice from an Alaskan glacier
Masood Ur Rehman Kayani et al.
MICROBIOME (2018)
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
Benjamin J. Tully et al.
SCIENTIFIC DATA (2018)
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes
Tom O. Delmont et al.
NATURE MICROBIOLOGY (2018)
Genome-centric view of carbon processing in thawing permafrost
Ben J. Woodcroft et al.
NATURE (2018)
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
Donovan H. Parks et al.
NATURE BIOTECHNOLOGY (2018)
MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis
Gherman V. Uritskiy et al.
MICROBIOME (2018)
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling
Ari Ugarte et al.
MICROBIOME (2018)
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Johannes Alneberg et al.
MICROBIOME (2018)
Unbiased Taxonomic Annotation of Metagenomic Samples
Bruno Fosso et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2018)
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
Yasuhiro Tanizawa et al.
BIOINFORMATICS (2018)
De novo assembly of viral quasispecies using overlap graphs
Jasmijn A. Baaijens et al.
GENOME RESEARCH (2017)
metaSPAdes: a new versatile metagenomic assembler
Sergey Nurk et al.
GENOME RESEARCH (2017)
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
Matthew R. Olm et al.
ISME JOURNAL (2017)
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M. Bowers et al.
NATURE BIOTECHNOLOGY (2017)
Shotgun metagenomics, from sampling to analysis
Christopher Quince et al.
NATURE BIOTECHNOLOGY (2017)
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Supratim Mukherjee et al.
NATURE BIOTECHNOLOGY (2017)
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software
Alexander Sczyrba et al.
NATURE METHODS (2017)
BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation
Cedric C. Laczny et al.
NUCLEIC ACIDS RESEARCH (2017)
Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist's Perspective - Not Only Size Matters!
John Vollmers et al.
PLOS ONE (2017)
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
Alexandra-Chloe Villani et al.
SCIENCE (2017)
GAMOLA2, a Comprehensive Software Package for the Annotation and Curation of Draft and Complete Microbial Genomes
Eric Altermann et al.
FRONTIERS IN MICROBIOLOGY (2017)
BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
Elaina D. Graham et al.
PEERJ (2017)
Atropos: specific, sensitive, and speedy trimming of sequencing reads
John P. Didion et al.
PEERJ (2017)
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Donovan H. Parks et al.
NATURE MICROBIOLOGY (2017)
Dynamics of the human gut microbiome in inflammatory bowel disease
Jonas Halfvarson et al.
NATURE MICROBIOLOGY (2017)
MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs
Dinghua Li et al.
BMC BIOINFORMATICS (2017)
cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing
Andrey Kechin et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2017)
Assembling metagenomes, one community at a time
Andries Johannes van der Walt et al.
BMC GENOMICS (2017)
ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins
Bertjan Broeksema et al.
BMC BIOINFORMATICS (2017)
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
Yu-Wei Wu et al.
BIOINFORMATICS (2016)
MetaQUAST: evaluation of metagenome assemblies
Alla Mikheenko et al.
BIOINFORMATICS (2016)
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage
Yun Kit Yeoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
Ron Caspi et al.
NUCLEIC ACIDS RESEARCH (2016)
Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens
Leighton Pritchard et al.
ANALYTICAL METHODS (2016)
MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression
Minji Kim et al.
BMC BIOINFORMATICS (2016)
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies
Shalabh Thakur et al.
BMC BIOINFORMATICS (2016)
SeqPurge: highly-sensitive adapter trimming for paired-end NGS data
Marc Sturm et al.
BMC BIOINFORMATICS (2016)
NCBI prokaryotic genome annotation pipeline
Tatiana Tatusova et al.
NUCLEIC ACIDS RESEARCH (2016)
Fast and sensitive taxonomic classification for metagenomics with Kaiju
Peter Menzel et al.
NATURE COMMUNICATIONS (2016)
Characterization of a Zika Virus Isolate from Colombia
Anismrita Lahon et al.
PLOS NEGLECTED TROPICAL DISEASES (2016)
Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes
Ankit Gupta et al.
FRONTIERS IN MICROBIOLOGY (2016)
Recovering complete and draft population genomes from metagenome datasets
Naseer Sangwan et al.
MICROBIOME (2016)
Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill
Nina Dombrowski et al.
NATURE MICROBIOLOGY (2016)
Genix: a new online automated pipeline for bacterial genome annotation
Frederico Schmitt Kremer et al.
FEMS MICROBIOLOGY LETTERS (2016)
Mash: fast genome and metagenome distance estimation using MinHash
Brian D. Ondov et al.
GENOME BIOLOGY (2016)
Evaluating techniques for metagenome annotation using simulated sequence data
Richard J. Randle-Boggis et al.
FEMS MICROBIOLOGY ECOLOGY (2016)
IVA: accurate de novo assembly of RNA virus genomes
Martin Hunt et al.
BIOINFORMATICS (2015)
NxTrim: optimized trimming of Illumina mate pair reads
Jared O'Connell et al.
BIOINFORMATICS (2015)
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Dinghua Li et al.
BIOINFORMATICS (2015)
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simao et al.
BIOINFORMATICS (2015)
SuRankCo: supervised ranking of contigs in de novo assemblies
Mathias Kuhring et al.
BMC BIOINFORMATICS (2015)
InteMAP: Integrated metagenomic assembly pipeline for NGS short reads
Binbin Lai et al.
BMC BIOINFORMATICS (2015)
PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm
Yun-Lung Li et al.
BMC BIOINFORMATICS (2015)
BEACON: automated tool for Bacterial GEnome Annotation ComparisON
Manal Kalkatawi et al.
BMC GENOMICS (2015)
The gut microbiome in health and in disease
Andrew B. Shreiner et al.
CURRENT OPINION IN GASTROENTEROLOGY (2015)
Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013
Simon J. Watson et al.
JOURNAL OF VIROLOGY (2015)
Microbial species delineation using whole genome sequences
Neha J. Varghese et al.
NUCLEIC ACIDS RESEARCH (2015)
An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data
Xutao Deng et al.
NUCLEIC ACIDS RESEARCH (2015)
COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets
Tungadri Bose et al.
PLOS ONE (2015)
Structure and function of the global ocean microbiome
Shinichi Sunagawa et al.
SCIENCE (2015)
Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes
Naseer Sangwan et al.
ENVIRONMENTAL MICROBIOLOGY REPORTS (2015)
IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites
Michalis Hadjithomas et al.
MBIO (2015)
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
Marcel Huntemann et al.
STANDARDS IN GENOMIC SCIENCES (2015)
Anvi'o: an advanced analysis and visualization platformfor 'omics data
A. Murat Eren et al.
PEERJ (2015)
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
Dongwan D. Kang et al.
PEERJ (2015)
Xander: employing a novel method for efficient gene-targeted metagenomic assembly
Qiong Wang et al.
MICROBIOME (2015)
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
Brett J. Baker et al.
MICROBIOME (2015)
Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
Ebrahim Afshinnekoo et al.
CELL SYSTEMS (2015)
Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces
Sean M. Gibbons et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2015)
MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
Afiahayati et al.
DNA RESEARCH (2015)
Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics
Zheng-Shuang Hua et al.
ISME JOURNAL (2015)
Expanded microbial genome coverage and improved protein family annotation in the COG database
Michael Y. Galperin et al.
NUCLEIC ACIDS RESEARCH (2015)
Update on RefSeq microbial genomes resources
Tatiana Tatusova et al.
NUCLEIC ACIDS RESEARCH (2015)
Metagenome-assembled genomes uncover a global brackish microbiome
Luisa W. Hugerth et al.
GENOME BIOLOGY (2015)
Omega: an Overlap-graph de novo Assembler for Metagenomics
Bahlul Haider et al.
BIOINFORMATICS (2014)
Prokka: rapid prokaryotic genome annotation
Torsten Seemann
BIOINFORMATICS (2014)
Trimmomatic: a flexible trimmer for Illumina sequence data
Anthony M. Bolger et al.
BIOINFORMATICS (2014)
QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform
Ram Krishna Shrestha et al.
BMC BIOINFORMATICS (2014)
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
Hongshan Jiang et al.
BMC BIOINFORMATICS (2014)
Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut
Jorge F. Vazquez-Castellanos et al.
BMC GENOMICS (2014)
The complete genome sequence for putative H2- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome
Kim M. Handley et al.
ENVIRONMENTAL MICROBIOLOGY (2014)
MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets
Rachamalla Maheedhar Reddy et al.
GENOMICS (2014)
Key roles for freshwater Actinobacteria revealed by deep metagenomic sequencing
Rohit Ghai et al.
MOLECULAR ECOLOGY (2014)
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
H. Bjorn Nielsen et al.
NATURE BIOTECHNOLOGY (2014)
Binning metagenomic contigs by coverage and composition
Johannes Alneberg et al.
NATURE METHODS (2014)
leeHom: adaptor trimming and merging for Illumina sequencing reads
Gabriel Renaud et al.
NUCLEIC ACIDS RESEARCH (2014)
Kraken: ultrafast metagenomic sequence classification using exact alignments
Derrick E. Wood et al.
GENOME BIOLOGY (2014)
PhyloSift: phylogenetic analysis of genomes and metagenomes
Aaron E. Darling et al.
PEERJ (2014)
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
Yu-Wei Wu et al.
MICROBIOME (2014)
Software for pre-processing Illumina next-generation sequencing short read sequences
Chuming Chen et al.
SOURCE CODE FOR BIOLOGY AND MEDICINE (2014)
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
Scott C. Clark et al.
BIOINFORMATICS (2013)
The automatic annotation of bacterial genomes
Emily J. Richardson et al.
BRIEFINGS IN BIOINFORMATICS (2013)
Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
Itai Sharon et al.
GENOME RESEARCH (2013)
ALIENTRIMMER: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads
Alexis Criscuolo et al.
GENOMICS (2013)
QcReads: An Adapter and Quality Trimming Tool for Next-Generation Sequencing Reads
Yunfei Ma et al.
JOURNAL OF GENETICS AND GENOMICS (2013)
Insights into the phylogeny and coding potential of microbial dark matter
Christian Rinke et al.
NATURE (2013)
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage
Mohamed F. Haroon et al.
NATURE (2013)
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
Mads Albertsen et al.
NATURE BIOTECHNOLOGY (2013)
Kraken: A set of tools for quality control and analysis Of high-throughput sequence data
Matthew P. A. Davis et al.
METHODS (2013)
TIGRFAMs and Genome Properties in 2013
Daniel H. Haft et al.
NUCLEIC ACIDS RESEARCH (2013)
An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis
Cristian Del Fabbro et al.
PLOS ONE (2013)
INDIGO - INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles
Intikhab Alam et al.
PLOS ONE (2013)
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment
Cindy J. Castelle et al.
NATURE COMMUNICATIONS (2013)
PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
Nicola Segata et al.
NATURE COMMUNICATIONS (2013)
Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota
Yongfei Hu et al.
NATURE COMMUNICATIONS (2013)
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
Todd J. Treangen et al.
GENOME BIOLOGY (2013)
An extended genovo metagenomic assembler by incorporating paired-end information
Afiahayati et al.
PEERJ (2013)
A de novo metagenomic assembly program for shotgun DNA reads
Binbin Lai et al.
BIOINFORMATICS (2012)
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
Yu Peng et al.
BIOINFORMATICS (2012)
GAGE: A critical evaluation of genome assemblies and assembly algorithms
Steven L. Salzberg et al.
GENOME RESEARCH (2012)
Individual genome assembly from complex community short-read metagenomic datasets
Chengwei Luo et al.
ISME JOURNAL (2012)
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Anton Bankevich et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Repetitive DNA and next-generation sequencing: computational challenges and solutions
Todd J. Treangen et al.
NATURE REVIEWS GENETICS (2012)
The Pfam protein families database
Marco Punta et al.
NUCLEIC ACIDS RESEARCH (2012)
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
Toshiaki Namiki et al.
NUCLEIC ACIDS RESEARCH (2012)
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
Daniel R. Mende et al.
PLOS ONE (2012)
NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data
Ravi K. Patel et al.
PLOS ONE (2012)
MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Jens Roat Kultima et al.
PLOS ONE (2012)
BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data
Pablo Pareja-Tobes et al.
PLOS ONE (2012)
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
Kelly C. Wrighton et al.
SCIENCE (2012)
Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota
Vaughn Iverson et al.
SCIENCE (2012)
The binning of rnetagenomic contings for physiology of mixed cultures
Marc Strous et al.
FRONTIERS IN MICROBIOLOGY (2012)
Ray Meta: scalable de novo metagenome assembly and profiling
Sebastien Boisvert et al.
GENOME BIOLOGY (2012)
Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem
Seungdae Oh et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)
Fast filtering for RNA homology search
Diana L. Kolbe et al.
BIOINFORMATICS (2011)
Meta-IDBA: a de Novo assembler for metagenomic data
Yu Peng et al.
BIOINFORMATICS (2011)
Quality control and preprocessing of metagenomic datasets
Robert Schmieder et al.
BIOINFORMATICS (2011)
Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies
Yong Kong
GENOMICS (2011)
A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using l-tuples
Yu-Wei Wu et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2011)
Genovo: De Novo Assembly for Metagenomes
Jonathan Laserson et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2011)
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
Rachel Mackelprang et al.
NATURE (2011)
SignalP 4.0: discriminating signal peptides from transmembrane regions
Thomas Nordahl Petersen et al.
NATURE METHODS (2011)
Sequence-specific error profile of Illumina sequencers
Kensuke Nakamura et al.
NUCLEIC ACIDS RESEARCH (2011)
Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets
Robert Schmieder et al.
PLOS ONE (2011)
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
Jarrod A. Chapman et al.
PLOS ONE (2011)
Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen
Matthias Hess et al.
SCIENCE (2011)
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
Daniel Aird et al.
GENOME BIOLOGY (2011)
Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt et al.
BMC BIOINFORMATICS (2010)
NGSQC: cross-platform quality analysis pipeline for deep sequencing data
Manhong Dai et al.
BMC GENOMICS (2010)
ACLAME: A CLAssification of Mobile genetic Elements, update 2010
Raphael Leplae et al.
NUCLEIC ACIDS RESEARCH (2010)
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Peter J. A. Cock et al.
NUCLEIC ACIDS RESEARCH (2010)
IMG ER: a system for microbial genome annotation expert review and curation
Victor M. Markowitz et al.
BIOINFORMATICS (2009)
Unsupervised statistical clustering of environmental shotgun sequences
Andrey Kislyuk et al.
BMC BIOINFORMATICS (2009)
ABySS: A parallel assembler for short read sequence data
Jared T. Simpson et al.
GENOME RESEARCH (2009)
Systematic artifacts in metagenomes from complex microbial communities
Vicente Gomez-Alvarez et al.
ISME JOURNAL (2009)
A core gut microbiome in obese and lean twins
Peter J. Turnbaugh et al.
NATURE (2009)
Genome Project Standards in a New Era of Sequencing
P. S. G. Chain et al.
SCIENCE (2009)
Consensus generation and variant detection by Celera Assembler
Gennady Denisov et al.
BIOINFORMATICS (2008)
The RAST server: Rapid annotations using subsystems technology
Ramy K. Aziz et al.
BMC GENOMICS (2008)
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino et al.
GENOME RESEARCH (2008)
Microbiology - Metagenomics
Philip Hugenholtz et al.
NATURE (2008)
A Bioinformatician's Guide to Metagenomics
Victor Kunin et al.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2008)
The Human Microbiome Project
Peter J. Turnbaugh et al.
NATURE (2007)
UniRef: comprehensive and non-redundant UniProt reference clusters
Baris E. Suzek et al.
BIOINFORMATICS (2007)
RNAmmer:: consistent and rapid annotation of ribosomal RNA genes
Karin Lagesen et al.
NUCLEIC ACIDS RESEARCH (2007)
Assessment of phylogenomic and orthology approaches for phylogenetic inference
B. E. Dutilh et al.
BIOINFORMATICS (2007)
Toward automatic reconstruction of a highly resolved tree of life
FD Ciccarelli et al.
SCIENCE (2006)
ISfinder: the reference centre for bacterial insertion sequences
P. Siguier et al.
NUCLEIC ACIDS RESEARCH (2006)
BASys: a web server for automated bacterial genome annotation
GH Van Domselaar et al.
NUCLEIC ACIDS RESEARCH (2005)
Comparative metagenomics of microbial communities
SG Tringe et al.
SCIENCE (2005)
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
R Overbeek et al.
NUCLEIC ACIDS RESEARCH (2005)
Community structure and metabolism through reconstruction of microbial genomes from the environment
GW Tyson et al.
NATURE (2004)
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
D Laslett et al.
NUCLEIC ACIDS RESEARCH (2004)
UniProt: the Universal Protein knowledgebase
R Apweiler et al.
NUCLEIC ACIDS RESEARCH (2004)
TETRA:: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences -: art. no. 163
H Teeling et al.
BMC BIOINFORMATICS (2004)
A phylogenomic approach to bacterial phylogeny:: Evidence of a core of genes sharing a common history
V Daubin et al.
GENOME RESEARCH (2002)
分享论文
