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The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio.

Wei N, Bemmels JB, Dick CW.

Mol Ecol Resour. 2014 Sep;14(5):953-65. doi: 10.1111/1755-0998.12245. Epub 2014 Mar 24.


Microsatellite marker discovery using single molecule real-time circular consensus sequencing on the Pacific Biosciences RS.

Grohme MA, Soler RF, Wink M, Frohme M.

Biotechniques. 2013 Nov;55(5):253-6. doi: 10.2144/000114104.


Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing.

Elliott CP, Enright NJ, Allcock RJ, Gardner MG, Meglécz E, Anthony J, Krauss SL.

Mol Ecol Resour. 2014 May;14(3):554-68. doi: 10.1111/1755-0998.12192. Epub 2013 Nov 29.


Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences.

Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P.

Am J Bot. 2012 Feb;99(2):193-208. doi: 10.3732/ajb.1100394. Epub 2011 Dec 20. Review.


Microsatellite DNA capture from enriched libraries.

Gonzalez EG, Zardoya R.

Methods Mol Biol. 2013;1006:67-87. doi: 10.1007/978-1-62703-389-3_5.


The accuracy, feasibility and challenges of sequencing short tandem repeats using next-generation sequencing platforms.

Zavodna M, Bagshaw A, Brauning R, Gemmell NJ.

PLoS One. 2014 Dec 1;9(12):e113862. doi: 10.1371/journal.pone.0113862. eCollection 2014.


ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research.

Pandey RV, Pabinger S, Kriegner A, Weinhäusel A.

BMC Bioinformatics. 2016 Feb 2;17:56. doi: 10.1186/s12859-016-0915-y.


A fault-tolerant method for HLA typing with PacBio data.

Chang CJ, Chen PL, Yang WS, Chao KM.

BMC Bioinformatics. 2014 Sep 3;15:296. doi: 10.1186/1471-2105-15-296.


Software for pre-processing Illumina next-generation sequencing short read sequences.

Chen C, Khaleel SS, Huang H, Wu CH.

Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8. eCollection 2014.


A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS.

Jiao X, Zheng X, Ma L, Kutty G, Gogineni E, Sun Q, Sherman BT, Hu X, Jones K, Raley C, Tran B, Munroe DJ, Stephens R, Liang D, Imamichi T, Kovacs JA, Lempicki RA, Huang DW.

J Data Mining Genomics Proteomics. 2013 Jul 31;4(3). pii: 16008.


The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms.

Larsen PA, Heilman AM, Yoder AD.

BMC Genomics. 2014 Aug 26;15:720. doi: 10.1186/1471-2164-15-720.


SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data.

Miller MP, Knaus BJ, Mullins TD, Haig SM.

J Hered. 2013 Nov-Dec;104(6):881-5. doi: 10.1093/jhered/est056. Epub 2013 Sep 19.


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

Meglécz E, Pech N, Gilles A, Dubut V, Hingamp P, Trilles A, Grenier R, Martin JF.

Mol Ecol Resour. 2014 Nov;14(6):1302-13. doi: 10.1111/1755-0998.12271. Epub 2014 May 26.


Optimizing selection of microsatellite loci from 454 pyrosequencing via post-sequencing bioinformatic analyses.

Fernandez-Silva I, Toonen RJ.

Methods Mol Biol. 2013;1006:101-20. doi: 10.1007/978-1-62703-389-3_7.


Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing.

Schoebel CN, Brodbeck S, Buehler D, Cornejo C, Gajurel J, Hartikainen H, Keller D, Leys M, Ríčanová S, Segelbacher G, Werth S, Csencsics D.

J Evol Biol. 2013 Mar;26(3):600-11. doi: 10.1111/jeb.12077. Epub 2013 Jan 17.


Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology.

Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo M, Weining S.

Am J Bot. 2012 Sep;99(9):e369-71. doi: 10.3732/ajb.1200077. Epub 2012 Aug 30.


No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing.

Westbrook CJ, Karl JA, Wiseman RW, Mate S, Koroleva G, Garcia K, Sanchez-Lockhart M, O'Connor DH, Palacios G.

Hum Immunol. 2015 Dec;76(12):891-6. doi: 10.1016/j.humimm.2015.03.022. Epub 2015 May 28.


A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y.

BMC Genomics. 2012 Jul 24;13:341. doi: 10.1186/1471-2164-13-341.


QC-Chain: fast and holistic quality control method for next-generation sequencing data.

Zhou Q, Su X, Wang A, Xu J, Ning K.

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.


Rapid development of microsatellite markers for Callosobruchus chinensis using Illumina paired-end sequencing.

Duan CX, Li DD, Sun SL, Wang XM, Zhu ZD.

PLoS One. 2014 May 16;9(5):e95458. doi: 10.1371/journal.pone.0095458. eCollection 2014.

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