MicrobeGPS Files

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Example Data
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Scope
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This folder contains example datasets for further analysis with MicrobeGPS. A
dataset consists of SAM files that can be directly loaded and analyzed with 
MicrobeGPS. You can compare your results to our results stored in the GPSA
file.

Download and unpack the zip file. Open MicrobeGPS and navigate to the unpacked
files to either analyze the SAM files or load the GPSA file.


1122 - STEC Human gut sample
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Human gut microbiome with possible Clostridium difficile infection. The 
original dataset is available from NCBI SRA with accession ERX237457. 
MicrobeGPS detects typical gut bacteria, including C. difficile.

Citation:
Loman, N. J. et al.: A culture-independent sequence-based metagenomics approach
to the investigation of an outbreak of Shiga-toxigenic Escherichia coli 
O104:H4. JAMA 309, 1502–1510 (2013).


LL-S1 - Lake Lanier freshwater metagenome
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First sample of a series of four freshwater metagenomes from Lake Lanier (USA).
Data is available from NCBI SRA accession SRX039150. Reads were mapped with
Bowtie 2 to NCBI Bacteria reference genomes; only a small fraction of the reads
could be mapped at all. This is reflected in the low validity MicrobeGPS 
calculates for the reference genomes.

Citation:
Oh, S. et al.: Metagenomic insights into the evolution, function, and 
complexity of the planktonic microbial community of Lake Lanier, a temperate
freshwater ecosystem. Applied and environmental microbiology 77, 6000–6011 
(2011).