Context

Cannabis is a genus of flowering plants in the family Cannabaceae.

Source: https://en.wikipedia.org/wiki/Cannabis

Content

In October 2016, Phylos Bioscience released a genomic open dataset of approximately 850 strains of Cannabis via the Open Cannabis Project. In combination with other genomics datasets made available by Courtagen Life Sciences, Michigan State University, NCBI, Sunrise Medicinal, University of Calgary, University of Toronto, and Yunnan Academy of Agricultural Sciences, the total amount of publicly available data exceeds 1,000 samples taken from nearly as many unique strains.

https://medium.com/google-cloud/dna-sequencing-of-1000-cannabis-strains-publicly-available-in-google-bigquery-a33430d63998

These data were retrieved from the National Center for Biotechnology Information’s Sequence Read Archive (NCBI SRA), processed using the BWA aligner and FreeBayes variant caller, indexed with the Google Genomics API, and exported to BigQuery for analysis. Data are available directly from Google Cloud Storage at gs://gcs-public-data--genomics/cannabis, as well as via the Google Genomics API as dataset ID 918853309083001239, and an additional duplicated subset of only transcriptome data as dataset ID 94241232795910911, as well as in the BigQuery dataset bigquery-public-data:genomics_cannabis.

All tables in the Cannabis Genomes Project dataset have a suffix like _201703. The suffix is referred to as [BUILD_DATE] in the descriptions below. The dataset is updated frequently as new releases become available.

The following tables are included in the Cannabis Genomes Project dataset:

Sample_info contains fields extracted for each SRA sample, including the SRA sample ID and other data that give indications about the type of sample. Sample types include: strain, library prep methods, and sequencing technology. See SRP008673 for an example of upstream sample data. SRP008673 is the University of Toronto sequencing of Cannabis Sativa subspecies Purple Kush.

MNPR01_reference_[BUILD_DATE] contains reference sequence names and lengths for the draft assembly of Cannabis Sativa subspecies Cannatonic produced by Phylos Bioscience. This table contains contig identifiers and their lengths.

MNPR01_[BUILD_DATE] contains variant calls for all included samples and types (genomic, transcriptomic) aligned to the MNPR01_reference_[BUILD_DATE] table. Samples can be found in the sample_info table. The MNPR01_[BUILD_DATE] table is exported using the Google Genomics BigQuery variants schema. This table is useful for general analysis of the Cannabis genome.

MNPR01_transcriptome_[BUILD_DATE] is similar to the MNPR01_[BUILD_DATE] table, but it includes only the subset transcriptomic samples. This table is useful for transcribed gene-level analysis of the Cannabis genome.

Fork this kernel to get started with this dataset.

Acknowledgements

Dataset Source: http://opencannabisproject.org/ Category: Genomics Use: This dataset is publicly available for anyone to use under the following terms provided by the Dataset Source - https://www.ncbi.nlm.nih.gov/home/about/policies.shtml - and is provided "AS IS" without any warranty, express or implied, from Google. Google disclaims all liability for any damages, direct or indirect, resulting from the use of the dataset. Update frequency: As additional data are released to GenBank View in BigQuery: https://bigquery.cloud.google.com/dataset/bigquery-public-data:genomics_cannabis View in Google Cloud Storage: gs://gcs-public-data--genomics/cannabis

Banner Photo by Rick Proctor from Unplash.

Inspiration

Which Cannabis samples are included in the variants table?

Which contigs in the MNPR01_reference_[BUILD_DATE] table have the highest density of variants?

How many variants does each sample have at the THC Synthase gene (THCA1) locus?