Portfolio

BreeDB database

Development of BreeDB into a mature product, in which more than one user, with different permissions, can work collaboratively (P1, PW, Figure 1).

Fig1-BreeDB
Figure 1, Elements of the BreeDB database, worked on in the VLPB-I project.

Analysis tools, which were designed as such that they can operate on both diploid and tetraploid crop species were implemented, including population structure determination (P4), association analysis (P5) and marker selection (P7). Visualization models were implemented for pedigrees (P3) and the three here fore mentioned analysis modules. In the framework of the VLPB-II project, methodologies are being implemented for a more optimal choice of breeding parents, chosen using segment specific profiles (combination of traits).

17 May, 2014

ELIXER FAIR and collaboration with DTL

In collaboration with DTL VLPB will act as one organization representing the interests of the VLPB members…

Galaxy

Based on the discussions and input from the VLBP associated companies…

GIBHUB

The Github environment was chosen and is used for development…

Snakemake framework

The de novo assembly, genome annotation, and variant calling pipeline…

Variant calling pipeline

A pipeline that takes NGS reads as input and which executes…

SNPCompare tool

Show a a cM or Mb based SNP density…

Allelic Variation Explorer (AVE)

A web-tool that allows visualization of single nucleotide polymorphisms (SNPs) by organizing…

White Paper Inventory NGS

An updatable inventory on technologies used in Next Generation Sequencing (NGS).

Redmine & Github VLPB Environment

An environment that contains all vlpb developed source code plus…

The VLPB Environment

Together with the VLPB Github environment a VLPB Google Group…

RNA run QC

A pipeline that takes NGS reads as input and produces a web page…

RNA counting pipeline

A pipeline for mapping and counting RNA seq reads including concentration spike-ins.

Size spike in visualization (small RNA-seq)

A visualization of counts of size spike-ins…

RNA experiment QC

A series of interactive visualizations using R-studio and a shiny-web server…

RNA normalization

A workflow to normalize RNA-seq experiments using spike-ins.