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FREQ-Seq: a rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations.

Chubiz LM, Lee MC, Delaney NF, Marx CJ.

PLoS One. 2012;7(10):e47959. doi: 10.1371/journal.pone.0047959. Epub 2012 Oct 31.


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

Campbell NR, Harmon SA, Narum SR.

Mol Ecol Resour. 2015 Jul;15(4):855-67. doi: 10.1111/1755-0998.12357. Epub 2014 Dec 25.


Validation of SNP allele frequencies determined by pooled next-generation sequencing in natural populations of a non-model plant species.

Rellstab C, Zoller S, Tedder A, Gugerli F, Fischer MC.

PLoS One. 2013 Nov 7;8(11):e80422. doi: 10.1371/journal.pone.0080422. eCollection 2013.


Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping.

Gautier M, Foucaud J, Gharbi K, Cézard T, Galan M, Loiseau A, Thomson M, Pudlo P, Kerdelhué C, Estoup A.

Mol Ecol. 2013 Jul;22(14):3766-79. doi: 10.1111/mec.12360. Epub 2013 Jun 4.


Synchronous waves of failed soft sweeps in the laboratory: remarkably rampant clonal interference of alleles at a single locus.

Lee MC, Marx CJ.

Genetics. 2013 Mar;193(3):943-52. doi: 10.1534/genetics.112.148502. Epub 2013 Jan 10.


Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

Kuhn A, Ong YM, Quake SR, Burkholder WF.

BMC Genomics. 2015 Jul 8;16:508. doi: 10.1186/s12864-015-1700-4.


High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq).

Preston JL, Royall AE, Randel MA, Sikkink KL, Phillips PC, Johnson EA.

BMC Genomics. 2016 Jun 14;17:464. doi: 10.1186/s12864-016-2669-3.


SNP discovery using Next Generation Transcriptomic Sequencing in Atlantic herring (Clupea harengus).

Helyar SJ, Limborg MT, Bekkevold D, Babbucci M, van Houdt J, Maes GE, Bargelloni L, Nielsen RO, Taylor MI, Ogden R, Cariani A, Carvalho GR; FishPopTrace Consortium., Panitz F.

PLoS One. 2012;7(8):e42089. doi: 10.1371/journal.pone.0042089. Epub 2012 Aug 7.


Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing.

Djari A, Esquerré D, Weiss B, Martins F, Meersseman C, Boussaha M, Klopp C, Rocha D.

BMC Genomics. 2013 May 7;14:307. doi: 10.1186/1471-2164-14-307.


Robust identification of local adaptation from allele frequencies.

Günther T, Coop G.

Genetics. 2013 Sep;195(1):205-20. doi: 10.1534/genetics.113.152462. Epub 2013 Jul 2.


SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?

Schunter C, Garza JC, Macpherson E, Pascual M.

Mol Ecol Resour. 2014 Jan;14(1):157-65. doi: 10.1111/1755-0998.12155. Epub 2013 Aug 31.


Genotyping-by-sequencing (GBS): a novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing.

De Donato M, Peters SO, Mitchell SE, Hussain T, Imumorin IG.

PLoS One. 2013 May 17;8(5):e62137. doi: 10.1371/journal.pone.0062137. Print 2013.


Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA.

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.

Retrovirology. 2013 Feb 13;10:18. doi: 10.1186/1742-4690-10-18.


Fast growth increases the selective advantage of a mutation arising recurrently during evolution under metal limitation.

Chou HH, Berthet J, Marx CJ.

PLoS Genet. 2009 Sep;5(9):e1000652. doi: 10.1371/journal.pgen.1000652. Epub 2009 Sep 18.


Novel high-speed droplet-allele specific-polymerase chain reaction: application in the rapid genotyping of single nucleotide polymorphisms.

Taira C, Matsuda K, Yamaguchi A, Sueki A, Koeda H, Takagi F, Kobayashi Y, Sugano M, Honda T.

Clin Chim Acta. 2013 Sep 23;424:39-46. doi: 10.1016/j.cca.2013.04.024. Epub 2013 May 17.


Gene mapping via bulked segregant RNA-Seq (BSR-Seq).

Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS.

PLoS One. 2012;7(5):e36406. doi: 10.1371/journal.pone.0036406. Epub 2012 May 7.


High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ System for simplified amplicon library preparation.

Moonsamy PV, Williams T, Bonella P, Holcomb CL, Höglund BN, Hillman G, Goodridge D, Turenchalk GS, Blake LA, Daigle DA, Simen BB, Hamilton A, May AP, Erlich HA.

Tissue Antigens. 2013 Mar;81(3):141-9. doi: 10.1111/tan.12071.


Fully automated pipeline for detection of sex linked genes using RNA-Seq data.

Michalovova M, Kubat Z, Hobza R, Vyskot B, Kejnovsky E.

BMC Bioinformatics. 2015 Mar 11;16:78. doi: 10.1186/s12859-015-0509-0.


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