PANATI is a tool for mapping and aligning short-read next generation resequencing data to a reference sequence for the purpose of detecting SNP variation, short insertions or deletions, and genotype calling across multiple samples. PANATI's design divides the mapping and alignment stage (primary analysis) from subsequent biological inquires (secondary analysis) by outputing an annotated version of the reference genome for subsequent use by separate programs focused solely on the biological question and the challenges inherent to it, rather than the tedious and time consuming parsing of alignments. Thus, PANATI's primary analysis stage might be viewed as a data compression technique in which the vast quantities of mostly redundant input data is reduced down to the essential information needed for many potential biological analyses. Presently, only SNP discovery and genotype calling across multiple samples is well developed but PANATI's primary analysis output is intended to be useful for other inquiries such as efficient RNA-seq expression analysis across multiple samples and detection of copy-number variable regions of the genome.

PANATI features

PANATI's development and release site is hosted by Presently there are no official release files and development version control systems are disabled and out of date since April 2012 while a manuscript describing PANATI is in review for publication.

PANATI is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with development versions of the gsl and zlib libraries installed. It may also compile and run on Mac OS X if gsl and zlib are installed.


Presently there is no peer-reviewed publication for PANATI. Authors of academic publications utilizing PANATI should cite PANATI as "Wright, MH. 2009-2012". A peer-reviewed is in review, please check back here for current information.

See also