标题
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
作者
关键词
Sunbeam, Shotgun metagenomic sequencing, Software, Pipeline, Quality control
出版物
Microbiome
Volume 7, Issue 1, Pages -
出版商
Springer Nature
发表日期
2019-03-22
DOI
10.1186/s40168-019-0658-x
参考文献
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。- Best practices for analysing microbiomes
- (2018) Rob Knight et al. NATURE REVIEWS MICROBIOLOGY
- MUMmer4: A fast and versatile genome alignment system
- (2018) Guillaume Marçais et al. PLoS Computational Biology
- Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates
- (2018) Joshua M. Taylor et al. PeerJ
- Viromes of one year old infants reveal the impact of birth mode on microbiome diversity
- (2018) Angela McCann et al. PeerJ
- Structure and function of the global topsoil microbiome
- (2018) Mohammad Bahram et al. NATURE
- T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency
- (2018) Erik L. Clarke et al. Genome Medicine
- Lack of detection of a human placenta microbiome in samples from preterm and term deliveries
- (2018) Jacob S. Leiby et al. Microbiome
- Evaluating the Information Content of Shallow Shotgun Metagenomics
- (2018) Benjamin Hillmann et al. mSystems
- Shotgun metagenomics, from sampling to analysis
- (2017) Christopher Quince et al. NATURE BIOTECHNOLOGY
- Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics
- (2017) Sonny T. M. Lee et al. Microbiome
- Optimizing methods and dodging pitfalls in microbiome research
- (2017) Dorothy Kim et al. Microbiome
- The Perioperative Lung Transplant Virome: Torque Teno Viruses Are Elevated in Donor Lungs and Show Divergent Dynamics in Primary Graft Dysfunction
- (2016) A. A. Abbas et al. AMERICAN JOURNAL OF TRANSPLANTATION
- Toward Accurate and Quantitative Comparative Metagenomics
- (2016) Stephen Nayfach et al. CELL
- Skin Microbiome Surveys Are Strongly Influenced by Experimental Design
- (2016) Jacquelyn S. Meisel et al. JOURNAL OF INVESTIGATIVE DERMATOLOGY
- MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices
- (2016) Dinghua Li et al. METHODS
- Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform
- (2016) Po-E Li et al. NUCLEIC ACIDS RESEARCH
- Fast and sensitive taxonomic classification for metagenomics with Kaiju
- (2016) Peter Menzel et al. Nature Communications
- Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
- (2016) Tom O. Delmont et al. PeerJ
- VSEARCH: a versatile open source tool for metagenomics
- (2016) Torbjørn Rognes et al. PeerJ
- Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota
- (2016) Abigail P. Lauder et al. Microbiome
- Human anelloviruses: an update of molecular, epidemiological and clinical aspects
- (2015) Sonia Spandole et al. ARCHIVES OF VIROLOGY
- Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease
- (2015) James D. Lewis et al. Cell Host & Microbe
- MetaPhlAn2 for enhanced metagenomic taxonomic profiling
- (2015) Duy Tin Truong et al. NATURE METHODS
- Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
- (2015) Tracey Allen K. Freitas et al. NUCLEIC ACIDS RESEARCH
- The Dfam database of repetitive DNA families
- (2015) Robert Hubley et al. NUCLEIC ACIDS RESEARCH
- Traces of ATCV-1 associated with laboratory component contamination
- (2015) Kristín Rós Kjartansdóttir et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Anvi’o: an advanced analysis and visualization platform for ‘omics data
- (2015) A. Murat Eren et al. PeerJ
- Prokka: rapid prokaryotic genome annotation
- (2014) T. Seemann BIOINFORMATICS
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- Rapid evaluation and quality control of next generation sequencing data with FaQCs
- (2014) Chien-Chi Lo et al. BMC BIOINFORMATICS
- A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples
- (2014) S. N. Naccache et al. GENOME RESEARCH
- Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets
- (2014) Y. Ma et al. JOURNAL OF VIROLOGY
- Fast and sensitive protein alignment using DIAMOND
- (2014) Benjamin Buchfink et al. NATURE METHODS
- Kraken: ultrafast metagenomic sequence classification using exact alignments
- (2014) Derrick E Wood et al. GENOME BIOLOGY
- Rapid evolution of the human gut virome
- (2013) S. Minot et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly
- (2012) Joanne B. Emerson et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Snakemake--a scalable bioinformatics workflow engine
- (2012) J. Koster et al. BIOINFORMATICS
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Human gut microbiome viewed across age and geography
- (2012) Tanya Yatsunenko et al. NATURE
- Metagenomic microbial community profiling using unique clade-specific marker genes
- (2012) Nicola Segata et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Primer3—new capabilities and interfaces
- (2012) Andreas Untergasser et al. NUCLEIC ACIDS RESEARCH
- dbCAN: a web resource for automated carbohydrate-active enzyme annotation
- (2012) Yanbin Yin et al. NUCLEIC ACIDS RESEARCH
- Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
- (2012) N. Fierer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
- (2012) Sahar Abubucker et al. PLoS Computational Biology
- Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
- (2012) Xochitl C Morgan et al. GENOME BIOLOGY
- RAPSearch: a fast protein similarity search tool for short reads
- (2011) Yuzhen Ye et al. BMC BIOINFORMATICS
- Integrative genomics viewer
- (2011) James T Robinson et al. NATURE BIOTECHNOLOGY
- Prodigal: prokaryotic gene recognition and translation initiation site identification
- (2010) Doug Hyatt et al. BMC BIOINFORMATICS
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
- (2010) Morgan N. Price et al. PLoS One
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
- (2009) K. D. Pruitt et al. GENOME RESEARCH
- JBrowse: A next-generation genome browser
- (2009) M. E. Skinner et al. GENOME RESEARCH
- Functional metagenomic profiling of nine biomes
- (2008) Elizabeth A. Dinsdale et al. NATURE
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreFind the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
Search