TASSEL pipeline

TASSEL specifications


Unique identifier OMICS_08865
Alternative name Trait Analysis by aSSociation, Evolution and Linkage
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 5.0
Stability Stable
Requirements Java
Maintained Yes


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  • person_outline Peter Bradbury <>

Publication for Trait Analysis by aSSociation, Evolution and Linkage

TASSEL IN pipelines

PMCID: 5912076
PMID: 29688387
DOI: 10.1093/database/bay037

[…] graphical representations provide quicker interpretation of information., when it comes to displaying snp diversity, several powerful desktop software applications already exist, most notably tassel (6) and flapjack (7), but stand-alone web-based visualization tools that can be easily implemented at web-based biological databases are not common, and snps are usually displayed […]

PMCID: 4761760
PMID: 26941944
DOI: 10.1002/ece3.1909

[…] library barcodes). raw data are available from ncbi, accession srp067014., initial data analysis used the zebra fish danio rerio, cyprinidae genome (ncbi assembly number grcz10) as reference for the tassel 4.3 pipeline (bradbury et al. 2007). however, as only ca. 4% of the reads mapped, this approach was abandoned in favor of the uneak3 pipeline (lu et al. 2013). tags were defined as groups […]

PMCID: 5069220
PMID: 27757948
DOI: 10.1186/s12284-016-0129-y

[…] asian cultivated rice (indica and japonica) was also observed, which actually also consistent with the clusters in nuclear genome test.fig. 3 , pca using the whole variation data was conducted in tassel, with the first two pcs explaining more than 81.9 % of the proportional variance; therefore, we constructed the pca using pc1 and pc2 (fig. 3c). four main groups were inferred, indica type, […]

PMCID: 5069220
PMID: 27757948
DOI: 10.1186/s12284-016-0129-y

[…] japonica type, african wild and cultivated rice, as well as several scattered accessions (asian wild rice) and admixed among them. multidimensional scaling (mds) analysis was also conducted with tassel, which reveals four major groups that were almost same with pca result (fig. 3d). even though no perfect clustering was found according to nuclear genome structure, these variations […]

PMCID: 5217118
PMID: 27866151
DOI: 10.1534/g3.116.035741

[…] 82 reference sequence (schmutz et al. 2010, http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=org_gmax) using the bwa 0.7.8-r455 program (li and durbin 2009). snps were called using the tassel 5.0 pipeline (bradbury et al. 2007) resulting in 33,728,018 tags for all 190 samples., a total of 27,672 snps were identified, with an average snp coverage of 10.98-fold. snps were filtered […]

TASSEL institution(s)
USA Department of Agriculture-Agricultural Research Service, Institute for Genomic Diversity, Cornell University, Ithaca, New York, and Cisco Systems, RTP, NC, USA

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