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Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis

Nicholas A. Tinker, Wubishet A. Bekele and Jiro Hattori
G3: Genes, Genomes, Genetics April 1, 2016 vol. 6 no. 4 857-863; https://doi.org/10.1534/g3.115.024596
Nicholas A. Tinker
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
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  • For correspondence: nick.tinker@canada.ca
Wubishet A. Bekele
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
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Jiro Hattori
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
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  • Figure 1
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    Figure 1

    Flow chart showing input files (green), output files (blue), and dependencies (connecting lines) associated with ‘Haplotag’ GBS discovery software. Default file names are shown in yellow, and are normally appended by “.txt” in the Windows file system. Three alternative pipelines (A, B, and C) are available, with required input labeled for each. The cluster discovery pipeline (A), and the haplotype discovery pipeline (B), start by aligning a complete inventory of tags (A), or a reduced inventory of tags from prior work (B), to produce clusters. In (B), the complete inventory is then realigned against this template to increase the sampling of new haplotypes. A complete tag-by-taxa matrix of tag counts (HTBT) is then formed for all tags belonging to clusters of two or more tags. Other output files are then created based on haplotype model fitting. In the production pipeline, only the files labeled by (C) are required, since genotyping is based on counting copies of haplotype-tags in the output files from previous discovery work.

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    Figure 2

    Passport file produced by Haplotag from simulated demonstration files. Here, six tags (potential haplotypes) are identified at the top. After model fitting by population-based filtering, two locus-models are selected. When Haplotag is run in ‘verbose’ mode, the details of model selection are written in a separate file (see File S2). Locus-1 contains three haplotypes and Locus-2 contains two. SNP positions are identified by color. The table at the bottom of the passport shows the tag counts at the presumed haplotypes within each locus. Counts greater than or equal to one are shaded, indicating that they are scored as “present”.

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  • Table 1 Comparison of GBS data analysis using UNEAK vs. Haplotag software
    SoftwareModeTime (hr:min)Number of Loci Passing Population Filter at Indicated Genotype CompletenessSNP Loci (80%) Duplicated by Alternate Pipeline
    Haplotype LociSNP loci
    50%80%50%80%NumberPercent
    UNEAKNA6:05NANA12,7804,2604204a99%a
    HaplotagCluster discovery6:54b29,42111,95043,37817,1174108c24%c
    HaplotagProduction0:11b24,412734331,6858872NANA
    • ↵a Number and percent of SNP-based loci called by UNEAK that were duplicated by Haplotag at the same 80% filtering level.

    • ↵b Times for Haplotag runs do not include the 6 hr required for generation of tag-count files using UNEAK.

    • ↵c Number and percent of SNP-based loci called by Haplotag that were duplicated by UNEAK at the same 80% filtering level.

Additional Files

  • Figures
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  • Supplemental Material for Tinker, Bekele, and Hattori, 2016

    Files in this Data Supplement:

    • File S1 - Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing (GBS) Analysis User Manual (2016-January-12). (.pdf, 776 KB)
    • File S2 - Details of model selection for: HC1. (.zip, 2 KB)
    • File S3 - This report shows legacy loci from other work including Huang et al 2014 that match consensus sequences in the current Haplotag production model. (.xlsx, 1.50 KB)
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Volume 6 Issue 4, April 2016

G3: Genes|Genomes|Genetics: 6 (4)

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Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis

Nicholas A. Tinker, Wubishet A. Bekele and Jiro Hattori
G3: Genes, Genomes, Genetics April 1, 2016 vol. 6 no. 4 857-863; https://doi.org/10.1534/g3.115.024596
Nicholas A. Tinker
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: nick.tinker@canada.ca
Wubishet A. Bekele
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jiro Hattori
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
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Citation

Haplotag: Software for Haplotype-Based Genotyping-by-Sequencing Analysis

Nicholas A. Tinker, Wubishet A. Bekele and Jiro Hattori
G3: Genes, Genomes, Genetics April 1, 2016 vol. 6 no. 4 857-863; https://doi.org/10.1534/g3.115.024596
Nicholas A. Tinker
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: nick.tinker@canada.ca
Wubishet A. Bekele
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jiro Hattori
Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ontario, K1A 0C6, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site

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