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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Jeffrey C. Glaubitz <>

Publication for TASSEL-GBS

TASSEL-GBS citations

 (69)
library_books

Genomic prediction applied to high biomass sorghum for bioenergy production

2018
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, […]

library_books

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.)

2018
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, […]

library_books

Genotyping by Sequencing and Genome–Environment Associations in Wild Common Bean Predict Widespread Divergent Adaptation to Drought

2018
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 […]

library_books

SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping by sequencing approach followed by Sequenom MassARRAY validation

2018
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. […]

library_books

Genome wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

2018
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 […]

library_books

Genome wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

2018
PMCID: 5764960
PMID: 29323254
DOI: 10.1038/s41598-017-18800-1

[…] sequencing of multiplexed gbs libraries were performed on illumina hiseq 2000 equipment, with 159 samples in two 96-well multiplex plates. single nucleotide polymorphisms were identified using the tassel-gbs pipeline in tassel software version 3.0.166. briefly, raw fastq sequences were trimmed to remove barcodes and reads from each of the four fastq files were collapsed into one master […]


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

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