msatcommander: detection of microsatellite repeat arrays and automated, locus‐specific primer design

By B. Faircloth. Molecular Ecology Resources, 2008

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Methods for Development of Microsatellite Markers: An Overview (2014, neutral): “With the availability of SSR mining tools like TROLL (Castelo et al., 2002), MISA (Thiel et al., 2003), SciRoKo (Kofler et al., 2007), Msatcommander (Faircloth, 2008), QDD (Meglécz et al., 2010) etc., it has now become a fast approach to search for microsatellite repeats in the EST sequences/…”
Applications of next generation sequencing in molecular ecology of non-model organisms (2011, background): “Microsatellite loci can be detected within NGS data sets with programs like msatcommander (Faircloth, 2008) and MSatFinder (Thurston and Field, 2005).”
Current trends in microsatellite genotyping (2011, methodology): “Software, such as MSATCOMMANDER (Faircloth 2008) or QDD (Meglécz et al.”
Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext) (2019, methodology): “We assembled reads from the eukaryotic libraries using the Geneious assembler (fastest setting), and we extracted contigs of 250 to 450 bp from eukaryotic libraries of tarantula, jellyfish, and coral for downstream microsatellite searches using msatCommander 1.0.8 ( Faircloth, 2008 ).”