NextGen Cassava Impact Report
The NextGen Cassava I\ mpact Report is here.
Cassavabase Errata
An issue with genotyping data has been fixed in the database. Certain genotyping protocols stored the dosage information with inverted ref and alt values. All protocols are now using consistent values. We recommend to re-download the data if you use it locally. [May 2, 2022]
Cassavabase Webinar
A Cassavabase Webinar will be given on Wednesday, March 23, at 8am EST, 12:00 GMT, 13:00 WAT/CET and 15:00 EAT. Zoom Link.
Product Profile Management
Manage product profiles on the site! Each breeding program can define product profiles on the respective breeding program manage page. [Nov 1, 2020]
Mixed Model tool
A tool for calculating mixed models is now available. [Nov 1, 2020]
K-Means Clustering
Run clustering on your trial genotype dataset from a trial detail page or the clustering page. [Oct 30, 2018]
ANOVA tool
Run ANOVA on your trait data, from a trial detail page. [March 01, 2018]
Cassava HapMap I and II viewer
You can search the cassava HapMaps whole genome sequencing data from Bredeson et al (2016) and Punna et al (2017) using Jbrowse by clicking the link above or by accessing the "Analyze" menu, "Hapmap Jbrowse" [June 6, 2017]
solGS: List of Trials
You can make a list of trials from the search wizard to create a combined training dataset. [Feb 24, 2017]
solGS: Queueing Analysis
For time consuming tasks in the solGS workflow, you can queue the tasks to run in the background and be notified by email when completed. [April 28, 2016]
Improved Search Wizard
The Search "Wizard" has been improved with faster speeds and new features, such as combining lists using intersection or union operators, starting with lists of accessions, and more. [February 21, 2016]
Faster upload speeds
Data uploads for trial information have been redesigned, making the process more intuitive, faster, and with better data quality checks. [February 21, 2016]
New trial feature available: physical layout viewer
The cassavabase trial detail page now displays a "Physical Trial Layout" feature where you can upload and view detailed physical trial coordinates. [October 3rd, 2015]
Cassavabase moved to secure http protocol
The Cassavabase server has been moved to a more secure protocol, https. Please let us know of any problems with this change. [Sept 27, 2015]
Cassava genome assembly v6 released
Today JGI released the new v6 cassava assembly with v6.1 annotations on Phytozome. The 582.25 Mb assembly comprises 18 chromosomes (plus unanchored scaffolds) and 33,033 genes (and 8,348 alternative transcripts). [May 20, 2015]
Genotypes loaded
5500 GBS genotypes have been loaded. [Feb 10, 2015]
Cassava genome v5.1 chromosome-scale genome assembly released!
The new version consists of the v4.1 scaffolds anchored onto the International Cassava Genetic Map Consortium framework and the pseudomolecule sequences can be downloaded from Phytozome. The Phytozome V10 gene models were mapped onto the v5.1 genome assembly.
Please cite: International Cassava Genetic Map Consortium. 2014. A 22,403 marker composite genetic linkage map for cassava (Manihot esculenta Crantz) derived from ten populations [bioRxiv]. Note that version v6.0 will be available in Feb 2015 which will include a new annotation.
CIAT releases data on Cassavabase
CIAT has released genotypic information for over 100 clones on Cassavabase.
Open Cassavabase Position
Cassavabase has an open position for a breeding bioinformatician.
Cassavabase site moved to a new location
The Cassavabase site was moved to a new location and IP address. Please let us know if there are any problems associated with this move. [July 12, 2013]
PlantCyc.org updates CassavaCyc
New release of the CassavaCyc (v.3.0) database with 491 metabolic pathways and 10000+ enzymes at the Plant Metabolic Network. [June 18, 2013]
IITA Data Released
IITA Ibadan phenotyping data for more than 2500 accessions released on Cassavabase [April 10, 2013]