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Readme.md

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Bird Microbiota Ecology Study
Kansas State University CIS BIO 734 Genomics and Bioinformatics

Started: April 2014

Project Team:

  • Denise Case (Computational & Information Sciences Department)
  • Kirsten Grond (Division of Biology)
  • Hamida Mahmood (Division of Biology)
  • Namoi Ohta (Division of Biology)
  • Allison Veatch (Division of Biology)

Quick Start Guide

Download the folder and subfolders.

Open sites.html in a browser.

Analysis

The project involved analyzing 538 paired-end read fastq files from Illumina with Mothur - an Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities.

Illumina: http://www.illumina.com/applications/sequencing/dna_sequencing.ilmn

Mothur: http://www.mothur.org/

Resources

The project uses:

Data-Driven Documents (d3.js) http://d3js.org/

Reusable-charts for d3.js (nvD3.js) http://nvd3.org/

Leaflet and Plugins http://leafletjs.com/ https://github.com/lvoogdt/Leaflet.awesome-markers

BootLeaf https://github.com/bmcbride/bootleaf

GINA Map Layers https://github.com/gina-alaska/gina-map-layers

Sample Sites

Samples where obtained from nine sites:

  1. Barrow
  2. Nome
  3. Cape Krusenstern
  4. Ikpikpuk River
  5. Colville
  6. Canning River
  7. Mackenzie River Delta
  8. Bylot Island
  9. Churchill

Locations

 | # | Country |     State | Coordinates                   | Latitude  | Longitude   |
 |---|---------|-----------|-------------------------------|-----------|-------------|
 | 1 |     USA |        AK | 71° 6'43.51"N 159° 4'7.73"W  | 71.112086 | -159.068814 |
 | 2 |     USA |        AK | 64°29'36.42"N 165°11'6.42"W  | 64.49345  | -165.185117 |
 | 3 |     USA |        AK | 67°25'2.09"N  163°52'27.26"W | 67.417247 | -163.874239 |
 | 4 |     USA |        AK | 71° 0'30.19"N 154°41'0.59"W  | 71.008386 | -154.683497 |
 | 5 |     USA |        AK | 70°33'34.03"N 148° 4'54.80"W | 70.559453 | -148.081889 |
 | 6 |     USA |        AK | 69°56'43.35"N 145° 5'53.35"W | 69.945375 | -145.098153 |
 | 7 |  Canada |        na | 68°48'57.34"N 137° 5'27.01"W | 68.815928 | -137.090836 |
 | 8 |  Canada |        na | 73°34'30.22"N  78°57'14.78"W | 73.575061 | -78.9541060 |
 | 9 |  Canada |        na | 58°46'15.13"N  94° 9'36.34"W | 58.770869 | -94.1600940 |