VAMPS Initiative

VAMPs initiativeMicrobiology of the Built Environment Boulder CO October 17th, 2012 Mitchell L. Sogin (sogin@mbl.edu) Andy Voorhis (voorhis@mbl.edu) Anna Shipunova (ashipunova@mbl.edu) Susan Huse (susan_huse@brown.edu) David Mark Welch (dmarkwelch@mbl.edu)

Sequence Independent rRNA or ITS Taxonomy Independent Sequences Quality Control, Trim to Anchor, De- multiplexTaxonomy Label GAST or Unique SLP Clustering OTUsQuality-Gast Dist RDP Sequences or UCLUST (master OTU set) Classifier Interactive Visualization and Analysis Inter-Community Intra-Community Analysis Analysis Heat Maps Pie Charts Dendrograms Bar Graphs Taxonomy Abundance Tables Sequence Diversity Trend Plots, PCoA Plots VAMPS DB Searching VAMPS DB Searching Taxon Searching

sogin•••••••

VAMPS Metadata CSV filerunkey (barcode) Only A,G,C,T - Length: Minimum 3nt; Maximum 12ntproject Name of the project: ONLY Alphanumeric and underscore _ (no spaces). Cannot start with a number.dataset Name of the dataset: ONLY Alphanumeric and underscore _ (no spaces). Cannot start with a number.sequence_direction NO COMMAS - Choose one: F, R or B for Forward, Reverse or Bothproject_title NO COMMAS - Free form brief title of the project (10 words orless).project_description NO COMMAS - All on one line, Greater detail than the title. Free form description of the project –a few sentences long.dataset_description NO COMMAS - brief description of the dataset.environmental_source_id A single id number selected from list

VAMPS Environmental Sample Source IDs in Metadata file:ID Sample Source ID Sample Source10 air 50 microbial_mat/biofilm20 extreme_habitat 60 miscellaneous_natural_or_artificial_environment30 host_associated 70 plant_associated40 human_associated 80 sediment41 human-skin 90 soil/sand42 human-oral 100 unknown43 human-gut 110 wastewater/sludge44 human-vaginal 120 water-freshwater45 human-amniotic_fluid 130 water-marine46 human-urine 140 indoor47 human-blood

runkeyprojectdatasetsequence directionproject titleproject description VAMPS Metadata csv filedataset descriptionenv. Source id

VAMPS Primers csv file

VAMPS sequence input file (fasta or fastq format)>FRZPY5Q02GAFHI rank=0000041 x=2462.0 y=84.0 length=117ACTGCCAACGCGCAGAACCTTACCAGGGCTTAAATGTAGTGGGACAGATTTTAGAGATAAATCCTTCTTCGGACTCATTACAAGGTGATGCATGGCCTAGCGTCGTAGACGGGCCGT>FRZPY5Q02IQ0Y3 rank=0000055 x=3471.0 y=797.0 length=101GCACGCTACGCGAAGAACCTTAACTAGACTTGACATCTCCTGAATTACTCTTAATCGAGGAAGCCCTTCGGGGCAGGAAGACAGGTGATGCATGGTTGTCG>FRZPY5Q02H6HTJ rank=0000060 x=3237.0 y=1317.0 length=93GCACGCAACGCGAAAAACCTTACCCGGGCTTGAAAGTTAGTGACCGCCGATGAAAGTTGGCTTTCCTTCGGGACACGAAACTAGGTGCTGCAT>FRZPY5Q02IIEZP rank=0000061 x=3373.0 y=467.0 length=105TCGCTAATTGGATTCAACGCCGGAAATCTTACCAGCTCCGACAGTAGCAATGACGCTCAGTGTGATGAGCTTGGTTGAGCTACTGAGAGGAGGTACATGGCTGTC>FRZPY5Q02ITXJA rank=0000063 x=3504.0 y=1140.0 length=104CTGTGCTAACCGATGAACCTCACCAGGTCTTGACATCTCCTGANAACCCTAGAGAT

http://vamps.mbl.edusogin@mbl.edu

VAMPS Initiative

by DavidCoil on Oct 19, 2012

Accessibility

Categories

Upload Details

Usage Rights

Statistics

VAMPS Initiative Presentation Transcript