Post on 04-Aug-2015
transcript
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)
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
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 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