title: HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.
abstract: BACKGROUND
  Microsatellites are among the most useful genetic markers in population biology. High-throughput sequencing of microsatellite-enriched libraries dramatically expedites the traditional process of screening recombinant libraries for microsatellite markers. However, sorting through millions of reads to distill high-quality polymorphic markers requires special algorithms tailored to tolerate sequencing errors in locus reconstruction, distinguish paralogous loci, rarify raw reads originating from the same amplicon and sort out various artificial fragments resulting from recombination or concatenation of auxiliary adapters. Existing programs warrant improvement.
  
  
  RESULTS
  We describe a microsatellite prediction framework named HighSSR for microsatellite genotyping based on high-throughput sequencing. We demonstrate the utility of HighSSR in comparison to Roche gsAssembler on two Roche 454 GS FLX runs. The majority of the HighSSR-assembled loci were reliably mapped against model organism reference genomes. HighSSR demultiplexes pooled libraries, assesses locus polymorphism and implements Primer3 for the design of PCR primers flanking polymorphic microsatellite loci. As sequencing costs drop and permit the analysis of all project samples on next-generation platforms, this framework can also be used for direct simple sequence repeats genotyping.
  
  
  BACKGROUND
  http://code.google.com/p/highssr/
authors.affiliation: New Mexico State University, Biology Deptartment, MSC 3AF, PO Box 30001, Las Cruces, NM 88003, USA. alexander@big.ac.cn
authors.forename: Alexander
authors.initials: A
authors.lastname: Churbanov
authors.forename: Rachael
authors.initials: R
authors.lastname: Ryan
authors.forename: Nabeeh
authors.initials: N
authors.lastname: Hasan
authors.forename: Donovan
authors.initials: D
authors.lastname: Bailey
authors.forename: Haofeng
authors.initials: H
authors.lastname: Chen
authors.forename: Brook
authors.initials: B
authors.lastname: Milligan
authors.forename: Peter
authors.initials: P
authors.lastname: Houde
mesh_terms: D000465:Algorithms; D000818:Animals; D002080:Butterflies / Q000145:classification / Q000235:genetics; D005658:Fungi / Q000145:classification / Q000235:genetics; D015723:Gene Library; D005819:Genetic Markers; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics; D005810:Multigene Family; D010944:Plants / Q000235:genetics; D011110:Polymorphism, Genetic; D013045:Species Specificity
chemical_list: D005819:Genetic Markers