This is the Linux app named iMSAT whose latest release can be downloaded as SSRs.zip. It can be run online in the free hosting provider OnWorks for workstations.
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iMSAT represents a full update of the vcf2MSAT program. This command line python program allows for a user to use the polymorphism data generated using SAM- and BAM-tools and a .fasta alignment file to search for polymorphic microsatellite markers (MSATs or STRs). By identifying polymorphic makers, rather than simple repeat regions as previous programs have done, iMSAT greatly increases the speed at which polymorphic MSATs that can be identified -- saving researchers precious time and money. Visit http://www.biomedcentral.com/1471-2164/15/858/abstract for the pdf article describing the utility of iMSAT and if you use the program please cite this article as: Andersen and Mills: iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries. BMC Genomics 2014 15:858.
- Polymorphic Microsatellite Identification
- Illumina Sequencing
- Genomic Analysis
This is an application that can also be fetched from https://sourceforge.net/projects/imsat/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.