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Fast sequence-based microsatellite genotyping development workflow

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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BEDTools: The Swiss‐Army Tool for Genome Feature Analysis

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Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae)

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Digital fragment analysis of short tandem repeats by high‐throughput amplicon sequencing

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CHIIMP : An automated high‐throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees

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SSR‐seq: Genotyping of microsatellites using next‐generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring

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Application of a SSR‐GBS marker system on investigation of European Hedgehog species and their hybrid zone dynamics

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Variation of Microsatellite Size Homoplasy Across Electromorphs, Loci, and Populations in Three Invertebrate Species

inferredcites →https://doi.org/10.1007/s00216-016-9536-6openalex-snapshot

A novel three-round multiplex PCR for SNP genotyping with next generation sequencing

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Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss)

inferredcites →https://doi.org/10.1007/s10592-018-1136-xopenalex-snapshot

Application of microsatellite genotyping by sequencing (SSR-GBS) to measure genetic diversity of the East African Oreochromis niloticus

inferredcites →https://doi.org/10.1007/s10709-011-9554-4openalex-snapshot

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.)

inferredcites →https://doi.org/10.1007/s11295-018-1295-4openalex-snapshot

Analysis of microsatellite loci in tree of heaven (Ailanthus altissima (Mill.) Swingle) using SSR-GBS

inferredcites →https://doi.org/10.1007/s12686-014-0352-zopenalex-snapshot

Characterization of thirteen new microsatellite markers for allis shad (Alosa alosa) and twaite shad (Alosa fallax)

inferredcites →https://doi.org/10.1016/j.cbpa.2015.01.025openalex-snapshot

The concentration of plasma metabolites varies throughout reproduction and affects offspring number in wild brown trout (Salmo trutta)

inferredcites →https://doi.org/10.1016/j.fsigen.2016.11.007openalex-snapshot

FDSTools: A software package for analysis of massively parallel sequencing data with the ability to recognise and correct STR stutter and other PCR or sequencing noise

inferredcites →https://doi.org/10.1016/j.gde.2017.01.012openalex-snapshot

A genomic view of short tandem repeats

inferredcites →https://doi.org/10.1016/j.tig.2006.06.009openalex-snapshot

Integrating patterns of polymorphism at SNPs and STRs

inferredcites →https://doi.org/10.1023/a:1005736722794openalex-snapshot

Identification and characterization of (GA/CT) n - microsatellite loci from Quercus petraea

inferredcites →https://doi.org/10.1038/hdy.2010.21openalex-snapshot

Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites

inferredcites →https://doi.org/10.1038/nature03959openalex-snapshot

Genome sequencing in microfabricated high-density picolitre reactors

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nrg.2017.115openalex-snapshot

Tandem repeats mediating genetic plasticity in health and disease

inferredcites →https://doi.org/10.1038/nrg1249openalex-snapshot

The evolution of molecular markers — just a matter of fashion?

inferredcites →https://doi.org/10.1038/nrg1707openalex-snapshot

Genotyping errors: causes, consequences and solutions

inferredcites →https://doi.org/10.1038/s41477-018-0172-3openalex-snapshot

Oak genome reveals facets of long lifespan

inferredcites →https://doi.org/10.1038/s41559-017-0347-8openalex-snapshot

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

inferredcites →https://doi.org/10.1038/srep43552openalex-snapshot

Genetic architecture of threshold reaction norms for male alternative reproductive tactics in Atlantic salmon (Salmo salar L.)

inferredcites →https://doi.org/10.1046/j.1365-2052.2001.0730b.xopenalex-snapshot

Thirty‐five polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss)

inferredcites →https://doi.org/10.1046/j.1365-294x.2002.01576.xopenalex-snapshot

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis

inferredcites →https://doi.org/10.1046/j.1365-294x.2003.02031.xopenalex-snapshot

Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species

inferredcites →https://doi.org/10.1093/bioinformatics/btp670openalex-snapshot

QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects

inferredcites →https://doi.org/10.1093/bioinformatics/btt593openalex-snapshot

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

inferredcites →https://doi.org/10.1093/bioinformatics/btu068openalex-snapshot

TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes

inferredcites →https://doi.org/10.1093/biomethods/bpx006openalex-snapshot

PrimerPooler: automated primer pooling to prepare library for targeted sequencing

inferredcites →https://doi.org/10.1093/gbe/evx164openalex-snapshot

Functional Mechanisms of Microsatellite DNA in Eukaryotic Genomes

inferredcites →https://doi.org/10.1093/gbe/evy244openalex-snapshot

Tandem Repeats Contribute to Coding Sequence Variation in Bumblebees (Hymenoptera: Apidae)

inferredcites →https://doi.org/10.1093/genetics/162.4.2025openalex-snapshot

Approximate Bayesian Computation in Population Genetics

inferredcites →https://doi.org/10.1093/molbev/msh212openalex-snapshot

Precision and Accuracy of Divergence Time Estimates from STR and SNPSTR Variation

inferredcites →https://doi.org/10.1093/molbev/msi093openalex-snapshot

Expressed Sequence Tag-Linked Microsatellites as a Source of Gene-Associated Polymorphisms for Detecting Signatures of Divergent Selection in Atlantic Salmon (Salmo salar L.)

inferredcites →https://doi.org/10.1098/rsos.150565openalex-snapshot

A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding

inferredcites →https://doi.org/10.1098/rsos.160651openalex-snapshot

Next Gen Pop Gen: implementing a high-throughput approach to population genetics in boarfish (Capros aper)

inferredcites →https://doi.org/10.1101/gr.177774.114openalex-snapshot

The landscape of human STR variation

inferredcites →https://doi.org/10.1101/gr.238602openalex-snapshot

SNPSTRs: Empirically Derived, Rapidly Typed, Autosomal Haplotypes for Inference of Population History and Mutational Processes

inferredcites →https://doi.org/10.1101/gr.5681207openalex-snapshot

Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers

inferredcites →https://doi.org/10.1111/1755-0998.12271openalex-snapshot

QDD version 3.1: a user‐friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate

inferredcites →https://doi.org/10.1111/1755-0998.12357openalex-snapshot

Genotyping‐in‐Thousands by sequencing (GT‐seq): A cost effective SNP genotyping method based on custom amplicon sequencing

inferredcites →https://doi.org/10.1111/1755-0998.12467openalex-snapshot

MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads

inferredcites →https://doi.org/10.1111/1755-0998.12561openalex-snapshot

megasat : automated inference of microsatellite genotypes from sequence data

inferredcites →https://doi.org/10.1111/1755-0998.12594openalex-snapshot

High‐throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low‐quantity and degraded DNA

inferredcites →https://doi.org/10.1111/2041-210x.13034openalex-snapshot

A cost‐and‐time effective procedure to develop SNP markers for multiple species: A support for community genetics

inferredcites →https://doi.org/10.1111/eva.12032openalex-snapshot

The sexually dimorphic on the Y‐chromosome gene (sdY) is a conserved male‐specific Y‐chromosome sequence in many salmonids

inferredcites →https://doi.org/10.1111/eva.12606openalex-snapshot

Genotyping‐by‐sequencing of genome‐wide microsatellite loci reveals fine‐scale harvest composition in a coastal Atlantic salmon fishery

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The evolving technology of DNA fingerprinting and its application to fisheries and aquaculture

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Polymorphic Atlantic salmon, Salmo salar L., microsatellites at the SSOSL438, SSOSL439 and SSOSL444 loci

inferredcites →https://doi.org/10.1111/j.1365-2052.2004.01091.xopenalex-snapshot

A microsatellite linkage map for Atlantic salmon (Salmo salar)

inferredcites →https://doi.org/10.1111/j.1365-294x.2004.02419.xopenalex-snapshot

Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion

inferredcites →https://doi.org/10.1111/j.1365-294x.2007.03829.xopenalex-snapshot

Genetic structure of an expanding Armillaria root rot fungus (Armillaria ostoyae) population in a managed pine forest in southwestern France

inferredcites →https://doi.org/10.1111/j.1471-8286.2004.00598.xopenalex-snapshot

Characterization and PCR multiplexing of novel highly variable tetranucleotide Atlantic salmon (Salmo salar L.) microsatellites

inferredcites →https://doi.org/10.1111/j.1471-8286.2005.00860.xopenalex-snapshot

Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship, population structure, and mixed‐fishery analyses

inferredcites →https://doi.org/10.1111/j.1600-0633.2006.00201.xopenalex-snapshot

Standardising multi‐laboratory microsatellite data in Pacific salmon: an historical view of the future

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Characterization of (GA)n Microsatellite Loci from Quercus Robur

inferredcites →https://doi.org/10.1111/j.1755-0998.2009.02750.xopenalex-snapshot

Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence

inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02891.xopenalex-snapshot

Application of single nucleotide polymorphisms to non‐model species: a technical review

inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02979.xopenalex-snapshot

Single‐nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

inferredcites →https://doi.org/10.1111/j.1755-0998.2011.02992.xopenalex-snapshot

High‐throughput microsatellite isolation through 454 GS‐FLX Titanium pyrosequencing of enriched DNA libraries

inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03002.xopenalex-snapshot

Comparison of random and SSR‐enriched shotgun pyrosequencing for microsatellite discovery and single multiplex PCR optimization inAcacia harpophyllaF. Muell. Ex Benth

inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03014.xopenalex-snapshot

Current trends in microsatellite genotyping

inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03036.xopenalex-snapshot

Genotyping HapSTR loci: phase determination from direct sequencing of PCR products

inferredcites →https://doi.org/10.1111/j.1755-0998.2011.03104.xopenalex-snapshot

Universal primers for fluorescent labelling of PCR fragments—an efficient and cost‐effective approach to genotyping by fluorescence

inferredcites →https://doi.org/10.1111/jfb.13149openalex-snapshot

From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome‐wide approaches in Atlantic salmon Salmo salar

inferredcites →https://doi.org/10.1111/jfb.13537openalex-snapshot

Estimating the effective number of breeders from single parr samples for conservation monitoring of wild populations of Atlantic salmon Salmo salar

inferredcites →https://doi.org/10.1111/mec.12138openalex-snapshot

Relative accuracy of three common methods of parentage analysis in natural populations

inferredcites →https://doi.org/10.1111/nph.13537openalex-snapshot

A community genetics perspective: opportunities for the coming decade

inferredcites →https://doi.org/10.1126/science.aan1425openalex-snapshot

DNA fragility in the parallel evolution of pelvic reduction in stickleback fish

inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

inferredcites →https://doi.org/10.1186/1471-2164-11-570openalex-snapshot

A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

inferredcites →https://doi.org/10.1186/1471-2164-6-50openalex-snapshot

A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects

inferredcites →https://doi.org/10.1371/journal.pgen.1003905openalex-snapshot

Robust Demographic Inference from Genomic and SNP Data

inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

inferredcites →https://doi.org/10.1371/journal.pone.0040699openalex-snapshot

Always Look on Both Sides: Phylogenetic Information Conveyed by Simple Sequence Repeat Allele Sequences

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.2144/000113156openalex-snapshot

Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR

inferredcites →https://doi.org/10.2144/000114052openalex-snapshot

A High-Plex PCR Approach for Massively Parallel Sequencing

inferredcites →https://doi.org/10.3389/fgene.2018.00073openalex-snapshot

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1111/1755-0998.13208openalex-snapshot

More affordable and effective noninvasive single nucleotide polymorphism genotyping using high‐throughput amplicon sequencing

inferred← citeshttps://doi.org/10.1111/eva.12922openalex-snapshot

Resolving fine‐scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

inferred← citeshttps://doi.org/10.1111/eva.12941openalex-snapshot

A river runs through it: The causes, consequences, and management of intraspecific diversity in river networks

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