These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
2. UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study. Qi P; Gimode D; Saha D; Schröder S; Chakraborty D; Wang X; Dida MM; Malmberg RL; Devos KM BMC Plant Biol; 2018 Jun; 18(1):117. PubMed ID: 29902967 [TBL] [Abstract][Full Text] [Related]
4. Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data. Torkamaneh D; Laroche J; Bastien M; Abed A; Belzile F BMC Bioinformatics; 2017 Jan; 18(1):5. PubMed ID: 28049422 [TBL] [Abstract][Full Text] [Related]
5. Skim-Based Genotyping by Sequencing Using a Double Haploid Population to Call SNPs, Infer Gene Conversions, and Improve Genome Assemblies. Bayer PE Methods Mol Biol; 2016; 1374():285-92. PubMed ID: 26519413 [TBL] [Abstract][Full Text] [Related]
6. GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-sequencing data. Melo AT; Bartaula R; Hale I BMC Bioinformatics; 2016 Jan; 17():29. PubMed ID: 26754002 [TBL] [Abstract][Full Text] [Related]
7. Genotyping-by-Sequencing and Its Application to Oat Genomic Research. Fu YB; Yang MH Methods Mol Biol; 2017; 1536():169-187. PubMed ID: 28132151 [TBL] [Abstract][Full Text] [Related]
8. Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies. Torkamaneh D; Laroche J; Belzile F PLoS One; 2016; 11(8):e0161333. PubMed ID: 27547936 [TBL] [Abstract][Full Text] [Related]
9. Role of NGS and SNP genotyping methods in sugarcane improvement programs. Manimekalai R; Suresh G; Govinda Kurup H; Athiappan S; Kandalam M Crit Rev Biotechnol; 2020 Sep; 40(6):865-880. PubMed ID: 32508157 [TBL] [Abstract][Full Text] [Related]
10. A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy. Wickland DP; Battu G; Hudson KA; Diers BW; Hudson ME BMC Bioinformatics; 2017 Dec; 18(1):586. PubMed ID: 29281959 [TBL] [Abstract][Full Text] [Related]
11. Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation. Brouard JS; Boyle B; Ibeagha-Awemu EM; Bissonnette N BMC Genet; 2017 Apr; 18(1):32. PubMed ID: 28381212 [TBL] [Abstract][Full Text] [Related]
12. Genotyping by Sequencing (GBS) for Genome-Wide SNP Identification in Plants. Pootakham W Methods Mol Biol; 2023; 2638():1-8. PubMed ID: 36781631 [TBL] [Abstract][Full Text] [Related]
13. Mining sequence variations in representative polyploid sugarcane germplasm accessions. Yang X; Song J; You Q; Paudel DR; Zhang J; Wang J BMC Genomics; 2017 Aug; 18(1):594. PubMed ID: 28793856 [TBL] [Abstract][Full Text] [Related]
14. An integrated SNP mining and utilization (ISMU) pipeline for next generation sequencing data. Azam S; Rathore A; Shah TM; Telluri M; Amindala B; Ruperao P; Katta MA; Varshney RK PLoS One; 2014; 9(7):e101754. PubMed ID: 25003610 [TBL] [Abstract][Full Text] [Related]
15. Application of Population Sequencing (POPSEQ) for Ordering and Imputing Genotyping-by-Sequencing Markers in Hexaploid Wheat. Edae EA; Bowden RL; Poland J G3 (Bethesda); 2015 Nov; 5(12):2547-53. PubMed ID: 26530417 [TBL] [Abstract][Full Text] [Related]
16. Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with New Combinations of Restriction Enzymes. Fu YB; Peterson GW; Dong Y G3 (Bethesda); 2016 Apr; 6(4):845-56. PubMed ID: 26818077 [TBL] [Abstract][Full Text] [Related]
17. SWEEP: A Tool for Filtering High-Quality SNPs in Polyploid Crops. Clevenger JP; Ozias-Akins P G3 (Bethesda); 2015 Jul; 5(9):1797-803. PubMed ID: 26153076 [TBL] [Abstract][Full Text] [Related]
20. A complete pipeline enables haplotyping and phasing macrohaplotype in long sequencing reads for polyploidy samples and a multi-source DNA mixture. Wang X; Muenzler M; King J; Liu M; Li H; Budowle B; Ge J Electrophoresis; 2024 May; 45(9-10):877-884. PubMed ID: 38196015 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]