SPARTA protocols

View SPARTA computational protocol

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chevron_left Read alignment Differential expression Adapter trimming Known transcript quantification Normalization Bioinformatics workflows Data visualization chevron_right
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SPARTA specifications


Unique identifier OMICS_09137
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Numpy, Java, R
Maintained Yes


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  • person_outline Robert B. Abramovitch <>

Publication for SPARTA

SPARTA in pipeline

PMCID: 5111405
PMID: 27935836
DOI: 10.1128/mBio.01691-16

[…] the truseq rna library preparation kit (illumina). libraries were sequenced using an illumina hiseq 2000 formulated for single-end, 50-nucleotide reads. analysis of sequence data was performed using sparta (simple program for automated reference-based bacterial rnaseq transcriptome analysis) (). briefly, raw reads were trimmed and assessed for quality using trimmomatic and fastqc, respectively […]

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SPARTA in publication

PMCID: 5554520
PMID: 28848532
DOI: 10.3389/fmicb.2017.01525

[…] coverage (ranging between 110× and 211× depending on the sample). aligned reads were then counted per gene in the etec h10407 genome using the htseq software suite. data were analyzed by using the sparta program (). differentially expressed genes were identified as those with an average normalized count >100, differential gene expression of >4.5-fold, and a p-value of <0.05. […]

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SPARTA institution(s)
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA; VANTAGE, Vanderbilt University, Nashville, TN, USA
SPARTA funding source(s)
Supported by grants to RBA from the NIH (R21AI105867) and the Bill & Melinda Gates Foundation (OPP1119065).

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