Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples

[1]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[2]  A. Clark The Human Microbiome. , 2017, The American journal of nursing.

[3]  Mattia D'Antonio,et al.  MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data , 2017, Bioinform..

[4]  Judith Breuer,et al.  Clinical and biological insights from viral genome sequencing , 2017, Nature Reviews Microbiology.

[5]  Shawn Rynearson,et al.  Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling , 2016, Genome Biology.

[6]  John Chilton,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update , 2016, Nucleic Acids Res..

[7]  Yi Zhang,et al.  VIP: an integrated pipeline for metagenomics of virus identification and discovery , 2016, Scientific Reports.

[8]  S. Rampelli,et al.  ViromeScan: a new tool for metagenomic viral community profiling , 2016, BMC Genomics.

[9]  M. Kuroda,et al.  VirusTAP: Viral Genome-Targeted Assembly Pipeline , 2016, Front. Microbiol..

[10]  Andrzej Zielezinski,et al.  5SRNAdb: an information resource for 5S ribosomal RNAs , 2015, Nucleic Acids Res..

[11]  Y. Cheung,et al.  Effect of complementary feeding with lipid-based nutrient supplements and corn-soy blend on the incidence of stunting and linear growth among 6- to 18-month-old infants and children in rural Malawi. , 2015, Maternal & child nutrition.

[12]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[13]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[14]  G. Weinstock,et al.  Metagenomic analysis of double-stranded DNA viruses in healthy adults , 2014, BMC Biology.

[15]  M. Kuroda,et al.  A food‐borne outbreak of gastroenteritis due to genotype G1P[8] rotavirus among adolescents in Japan , 2014, Microbiology and immunology.

[16]  R. Edwards,et al.  A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes , 2014, Nature Communications.

[17]  S. Salminen,et al.  Presence of Human Enteric Viruses in the Stools of Healthy Malawian 6-Month-Old Infants , 2014, Journal of pediatric gastroenterology and nutrition.

[18]  T. Sharpton An introduction to the analysis of shotgun metagenomic data , 2014, Front. Plant Sci..

[19]  François Enault,et al.  Metavir 2: new tools for viral metagenome comparison and assembled virome analysis , 2014, BMC Bioinformatics.

[20]  Fredrik Vannberg,et al.  KAnalyze: a fast versatile pipelined K-mer toolkit , 2014, Bioinform..

[21]  Anton Nekrutenko,et al.  Dissemination of scientific software with Galaxy ToolShed , 2014, Genome Biology.

[22]  Paola Bonizzoni,et al.  Further Steps in TANGO: improved taxonomic assignment in metagenomics , 2014, Bioinform..

[23]  Susan Holmes,et al.  phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data , 2013, PloS one.

[24]  M. Facciotti,et al.  An Integrated Pipeline for de Novo Assembly of Microbial Genomes , 2012, PloS one.

[25]  Daniel J. Nasko,et al.  VIROME: a standard operating procedure for analysis of viral metagenome sequences , 2012, Standards in genomic sciences.

[26]  Siu-Ming Yiu,et al.  IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth , 2012, Bioinform..

[27]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[28]  Leping Li,et al.  ART: a next-generation sequencing read simulator , 2012, Bioinform..

[29]  François Enault,et al.  Metavir: a web server dedicated to virome analysis , 2011, Bioinform..

[30]  Hideaki Tanaka,et al.  MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads , 2011, BCB '11.

[31]  Robert C. Edgar,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2001 .

[32]  Konrad H. Paszkiewicz,et al.  De novo assembly of short sequence reads , 2010, Briefings Bioinform..

[33]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[34]  Steven J. M. Jones,et al.  Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .

[35]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[36]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[37]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[38]  R. Knight,et al.  The Human Microbiome Project , 2007, Nature.

[39]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[40]  Edward M. Rubin,et al.  Metagenomics: DNA sequencing of environmental samples , 2005, Nature Reviews Genetics.

[41]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[42]  W. Bossert,et al.  The Measurement of Diversity , 2001 .

[43]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.