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BiomeSeq: A Tool for the Characterization of Animal Microbiomes from Metagenomic Data

https://doi.org/10.1101/800995
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.chom.2015.03.008openalex-snapshot
The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development
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Assessing Species Diversity Using Metavirome Data: Methods and Challenges
inferredcites →https://doi.org/10.1016/j.mimet.2011.03.014openalex-snapshot
Rethinking microbial diversity analysis in the high throughput sequencing era
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Viral potentiation of bacterial superinfection of the respiratory tract
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
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Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
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Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
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Virus-specific CD8+ T cells accumulate near sensory nerve endings in genital skin during subclinical HSV-2 reactivation
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Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/ve/vew022openalex-snapshot
Challenges in the analysis of viral metagenomes
inferredcites →https://doi.org/10.1099/jmm.0.000047openalex-snapshot
Longitudinal monitoring for respiratory pathogens in broiler chickens reveals co-infection of Chlamydia psittaci and Ornithobacterium rhinotracheale
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1109/52.363167openalex-snapshot
Realities of off-shore reengineering
inferredcites →https://doi.org/10.1111/j.2041-210x.2011.00169.xopenalex-snapshot
phytools: an R package for phylogenetic comparative biology (and other things)
inferredcites →https://doi.org/10.1111/mec.12481openalex-snapshot
Towards a unified paradigm for sequence‐based identification of fungi
inferredcites →https://doi.org/10.1128/aem.00362-18openalex-snapshot
A Consistent and Predictable Commercial Broiler Chicken Bacterial Microbiota in Antibiotic-Free Production Displays Strong Correlations with Performance
inferredcites →https://doi.org/10.1128/aem.01043-13openalex-snapshot
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/cmr.17.4.840-862.2004openalex-snapshot
Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases
inferredcites →https://doi.org/10.1164/rccm.201602-0220ocopenalex-snapshot
Nasopharyngeal Microbiota, Host Transcriptome, and Disease Severity in Children with Respiratory Syncytial Virus Infection
inferredcites →https://doi.org/10.1186/1471-2105-12-35openalex-snapshot
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot
The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes
inferredcites →https://doi.org/10.1186/gm467openalex-snapshot
The human mycobiome in health and disease
inferredcites →https://doi.org/10.1186/s12866-017-1092-5openalex-snapshot
Upper and lower respiratory tract microbiota in horses: bacterial communities associated with health and mild asthma (inflammatory airway disease) and effects of dexamethasone
inferredcites →https://doi.org/10.1186/s40168-016-0177-yopenalex-snapshot
Research on the human virome: where are we and what is next
inferredcites →https://doi.org/10.1371/journal.pone.0129059openalex-snapshot
Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data
inferredcites →https://doi.org/10.1371/journal.pone.0131578openalex-snapshot
Geographic Analysis of Urologist Density and Prostate Cancer Mortality in the United States
inferredcites →https://doi.org/10.1371/journal.pone.0178247openalex-snapshot
Acute exercise does not modify brain activity and memory performance in APP/PS1 mice
inferredcites →https://doi.org/10.1371/journal.pone.0188455openalex-snapshot
Age-related differences in the respiratory microbiota of chickens
inferredcites →https://doi.org/10.1371/journal.ppat.1006292openalex-snapshot
The blood DNA virome in 8,000 humans
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.3168/jds.2016-11522openalex-snapshot
Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics
inferredcites →https://doi.org/10.3201/eid1410.080119openalex-snapshot
Microbial Interactions during Upper Respiratory Tract Infections
inferredcites →https://doi.org/10.3382/ps/pev010openalex-snapshot
Microbial communities present in the lower respiratory tract of clinically healthy birds in Pakistan
inferredcites →https://doi.org/10.3389/fmicb.2016.00459openalex-snapshot
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
inferredcites →https://doi.org/10.3390/ijms12117861openalex-snapshot
Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

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inferred← citeshttps://doi.org/10.3390/microorganisms9040721openalex-snapshot
Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing
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