TASSEL-GBS protocols

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TASSEL-GBS specifications

Information


Unique identifier OMICS_08634
Name TASSEL-GBS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Jeffrey C. Glaubitz <>

Publication for TASSEL-GBS

TASSEL-GBS in pipelines

 (4)
2017
PMCID: 5293825
PMID: 28223988
DOI: 10.3389/fpls.2017.00089

[…] using these criteria, an estimated error rate of less than 0.01 was obtained. the r-package “pegas” and custom perl scripts were used for calculating the heterozygosity of variants., for the tassel-gbs pipeline, a tassel_plugin interface with default parameters was used to call snps (figure , intermediate). tag counts were generated from fastq files with the fastqtotagcountplugin. […]

2016
PMCID: 5147965
PMID: 27936008
DOI: 10.1371/journal.pone.0167715

[…] were removed using 1.8x volumes of the agencourt ampure beads (beckman coulter). each gbs library was sequenced on one lane of a hiseq 2000 illumina sequencing system., snps were called using the tassel-gbs pipeline build 5.2.10 []. bowtie2 was used to align illumina reads to the c. pepo zucchini genome draft v3.2 pre-released by a joint effort of the genomics and bioinformatics and cucurbits […]

2015
PMCID: 4646766
PMID: 26601206
DOI: 10.1126/sciadv.1400218

[…] icrisat, india (icrisat accessions), and seedling tissue was used for dna extraction. dna preparation and genotyping-by-sequencing were carried out as described in (). snp calls were made using the tassel gbs pipeline version 3.0 () using the sorghum bicolor genome v1.4 from phytozome as a reference (, ) and bwa as the alignment algorithm (). the gbs approach produces a large fraction […]

2015
PMCID: 5386344
PMID: 25942004
DOI: 10.1038/srep09468

[…] with read lengths of 100-bp using hiseq2000 (illumina inc., san diego, ca, usa) ngs platform. the fastq raw sequence reads were processed for high-quality sequence filtering and mapping through tassel-gbs. the sequence reads with a minimum phred q-score of 10 across the first 72-bp nucleotide sequences were considered as high-quality, which were further rechecked for their quality using […]


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TASSEL-GBS in publications

 (68)
PMCID: 5893689
PMID: 29670457
DOI: 10.1007/s11032-018-0802-5

[…] standard gbs protocol (elshire et al. ) with restriction enzyme apeki and 96-plex approach. we then used the bwa (li and durbin ) to align tags to the reference genome of sorghum bicolor (v2.1) and tassel-gbs (glaubitz et al. ) pipeline for snp calling., we initially assessed the quality of these genotypic data with the following statistics: frequency of heterozygous genotypes for each snp, […]

PMCID: 5869928
PMID: 29616069
DOI: 10.3389/fpls.2018.00362

[…] (gcwgc) and sequenced twice with the illumina hiseq (illumina inc. san diego, ca) next-generation sequencing platform at the cornell genomic diversity facility., snp calling was performed using the tassel-gbs pipeline v5.0 (bradbury et al., ). a filtered hapmap was created with the following parameters: minimum minor allele frequency (mnmaf) of 0.05, minimum locus coverage (mnlcov) of 0.8, […]

PMCID: 5826387
PMID: 29515597
DOI: 10.3389/fpls.2018.00128

[…] order to eliminate correlations among these., the raw illumina dna sequence data (180,540,321 high-quality barcoded reads per lane) were processed through the gbs analysis pipeline as implemented in tassel-gbs v3.0. the gbs analysis generated 1,625,330 unique sequence clusters (tags, ; ). of the total number of tags, 71.2% aligned uniquely to the p. vulgaris reference genome, 10.1% had multiple […]

PMCID: 5819801
PMID: 29462210
DOI: 10.1371/journal.pone.0193121

[…] to 64 bp sequence tags and aligned to the 12x v. vinifera ‘pn40024’ reference genome [,] using burrows-wheeler aligner maximal exact match using default parameters []. snps were called using tassel-gbs pipeline, v3.0.166 []. the variant call format (vcf) output file [] consisted of 509,293 snps that were present in >90% of the progeny and had a minor allele frequency >0.01. […]

PMCID: 5784162
PMID: 29367617
DOI: 10.1038/s41598-018-19696-1

[…] to standard procedures using the dnaeasy plant mini extraction kit. gbs libraries were constructed using the apeki restriction enzyme as previously described. marker genotypes were called using tassel gbs pipeline v4 after aligning the reads to the cassava v6 reference genome,. markers with more than 60% missing calls were removed., the resulting marker dataset consisted of 173,647 […]


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TASSEL-GBS institution(s)
Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA

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