SRA2R, a package to import SRA data directly into R
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inst/unitTests
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DESCRIPTION
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NAMESPACE
README.md
ReferenceVsDepth.pdf
RunAccessions.txt
SRA2R.Rproj

README.md

SRA2R

SRA2R, a package to import SRA data directly into R

This package is not maintained and is currently not functional.

SRA ToolKit examples

sra-stat example

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sra-stat

(known good but large)
sra-stat --quick --xml SRR390728
(smaller file)
sra-stat --quick --xml SRR2971307
(small and no alignment)
sra-stat --quick --xml ERR1162649

sra-pileup

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sra-pileup

Command-line

sra-pileup -r chr20:1530960-1540960 SRR2971307

In R

x = read.delim(text = system('~/sratoolkit.2.5.7-ubuntu64/bin/sra-pileup -r chr20:1530960-1540960 SRR2971307',intern=TRUE))

ncbi ngs SDK details

  • /usr/include/ngs (interfaces for C++ ngs)
  • /usr/include/ncbi-vdb (NGS.hpp)
  • /usr/local/share/doc/ngs (javadoc)
  • LD_LIBRARY_PATH = /usr/local/ngs/ngs-sdk/lib64:/usr/local/ncbi/ncbi-vdb/lib64:

R and Rcpp documentation of interest