<p>Hi friends,</p>

<p>I am working on a population genetic project using microsatellite markers. Due to the large sample size and 12 microsatellite loci, I will need to use an efficient and solid method/tool to score the fragment analysis data (.fsa file type) from genetic analyzer 3130. In total, I will have nearly 5000 files to be scored. I have done part of my pilot fragment analysis results with a free version software, PeakScanner 1.0 (ABI); however, this software doesn't come with automatic features, and thus I have to score the data manually, which is very time consuming and inconvenient. In addition, we don't have the budget to purchase some commercial softwares (such as, Gene Mapper ) to do this. I am wondering if you guys can give me some suggestions to handle this situation.</p>

<p>OR</p>

<p>I can keep the question short, any substitution software package for ABI GeneMapper to score multiplex fragment analysis data (*.fsa)?</p>

<p>Thank you very much.</p>

Update for this question:

There's a package called `Fragman` in R just released in 2015, performs fragment analysis using FSA files: https://cran.r-project.org/web/packages/Fragman/