ArticleBioinformatics (Oxford, England)2012
HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools.Frontiers in genetics · 2024Review
- The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century.Applications in plant sciences · 2016Article
- PSR: polymorphic SSR retrieval.BMC research notes · 2015Article
- Genetic diversity and association mapping of bacterial blight and other horticulturally important traits with microsatellite markers in pomegranate from India.Molecular genetics and genomics : MGG · 2015Article
- ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection.Database : the journal of biological databases and curation · 2015Article
- Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies.Bioinformatics and biology insights · 2015Review
- pSTR Finder: a rapid method to discover polymorphic short tandem repeat markers from whole-genome sequences.Investigative genetics · 2015Article
- Challenges in analysis and interpretation of microsatellite data for population genetic studies.Ecology and evolution · 2014Review
- VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.Nucleic acids research · 2014Article
- Genomic and global approaches to unravelling how hypermutable sequences influence bacterial pathogenesis.Pathogens (Basel, Switzerland) · 2014Review
- A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance.International journal of molecular sciences · 2013Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationMicrosatellites 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.
resultsWe 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. AVAILABILITY: http://code.google.com/p/highssr/
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.