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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.
Features
- Polymorphic Microsatellite Identification
- Illumina Sequencing
- Genomic Analysis
Project Samples
Categories
Bio-InformaticsLicense
Creative Commons Attribution LicenseFollow iMSAT
User Reviews
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Version 1.1 of this program is completely broken. The developers commented out critical code during their internal testing and forgot to uncomment it when they finished - meaning if you plan to use this on any standard FASTA file you will have to fix the python code before you can use the program. However the code also cannot read standard VCF files because of a bad assumption in the program's logic (it assumes every line of a VCF will contain a tab in it and the program will crash if it finds any line without a tab in it). I will be happy to update my review once the project has been updated but my attempts to contact the developers have so far gone ignored and I want this to serve as a warning to others to save them the trouble of finding these errors themselves.
