Figure 1
From: iMSAT: a novel approach to the development of microsatellite loci using barcoded Illumina libraries
iMSAT workflow diagram. Before using iMSAT, barcoded NGS sequencing libraries are produced (A) and sequenced (B) and either used to create a de novo assembly or to align an available reference genome (C). Then using SAMtools and BWA the individual sequence reads are used to create a polymorphism report (D) that includs the location of the polymorphic loci, type (SNP or INDEL), and other quality statistics. iMSAT then uses the output and the alignment file to filter the polymorphism data based on a user specified number of base pairs (E), identifies the STR motifs and the number of repeats (F), and outputs separate .FASTA preprocessing files for each candidate locus that can be used with primer design software (G).