vamps initiative

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Mitchell L. Sogin ([email protected]) Andy Voorhis ([email protected]) Anna Shipunova ([email protected]) Susan Huse ([email protected]) David Mark Welch ([email protected] VAMPs initiative Microbiology of the Built Environment Boulder CO October 17 th , 2012

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Mitchell L. Sogin ([email protected])Andy Voorhis ([email protected])Anna Shipunova ([email protected])Susan Huse ([email protected])David Mark Welch ([email protected])

VAMPs initiativeMicrobiology of the Built Environment

Boulder COOctober 17th, 2012

rRNA or ITSSequences

Taxonomy IndependentSequence Independent

GAST or

RDP Classifier

SLP Clustering

or UCLUST

Quality Control, Trim to Anchor, De-multiplex

OTUs(master OTU set)

Taxonomy LabelQuality-Gast Dist

UniqueSequences

Interactive Visualization and Analysis

Inter-CommunityAnalysis

Intra-CommunityAnalysis

Heat MapsDendrogramsTaxonomy Abundance TablesTrend Plots, PCoA PlotsVAMPS DB Searching

Pie Charts Bar GraphsSequence DiversityVAMPS DB SearchingTaxon Searching

sogin•••••••

runkey (barcode) Only A,G,C,T - Length: Minimum 3nt; Maximum 12nt

project 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 or less).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 Metadata CSV file

ID Sample Source 10 air 20 extreme_habitat 30 host_associated 40 human_associated 41 human-skin 42 human-oral 43 human-gut 44 human-vaginal 45 human-amniotic_fluid 46 human-urine 47 human-blood

ID Sample Source 50 microbial_mat/biofilm 60 miscellaneous_natural_or_artificial_environment 70 plant_associated 80 sediment 90 soil/sand 100 unknown 110 wastewater/sludge 120 water-freshwater 130 water-marine 140 indoor

VAMPS Environmental Sample Source IDs in Metadata file:

runk

ey

proj

ect

data

set

sequ

ence

dire

ction

proj

ect ti

tle

proj

ect d

escr

iptio

n

data

set d

escr

iptio

n

env.

Sou

rce

id

VAMPS Metadata csv file

VAMPS Primers csv file

VAMPS sequence input file (fasta or fastq format) >FRZPY5Q02GAFHI rank=0000041 x=2462.0 y=84.0 length=117 ACTGCCAACGCGCAGAACCTTACCAGGGCTTAAATGTAGTGGGACAGATTTTAGAGATAAATCCTTCTTCGGACTCATTACAAGGTGATGCATGGCCTAGCGTCGTAGACGGGCCGT

>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=104CTGTGCTAACCGATGAACCTCACCAGGTCTTGACATCTCCTGANAACCCTAGAGATAGGGNGTTCCCCTTCGGGGGACAGGATGACAGGTGCTGCATGGTCGTC >FRZPY5Q02IYHYK rank=0000072 x=3556.0 y=1242.0 length=97GACAGCAACGCGAAAAACCTTACCTACAATTGACATACTGCGAATTTTCTAGAGATAGATTAGTGCCTTCGGAACGCAGATACAGGTGATGCATGGT