Our Activities
Genotyping by Sequencing
This activity is in collaboration with the Cornell University (Ithaca, NY, USA). We get provided the raw sequencing (fastq) files as well as the variant calling (vcf) files containing the predicted SNPs.
Bioinformatics IITA has the knowledge and capacity to run the SNP discovery from the raw sequencing files using either the tassel5 or the GATK workflow. Any downstream analysis such as the SNP filtering, association and population studies can be applied using the bioinformatics servers.
We are hosting more than 200 raw sequencing files, data of more than 20’000 samples from cassava all over Africa.
DNA Methylation profiling
We have in investigation some cassava genotypes we expect a certain epigenetic effect determining the observed trait. We are analyze the whole genome DNA methylation via bisulfide treatment and sequencing. Comparing the different DNA methylation profiles will lead us to regions which are differentially methylated. Integrating gene expression and small RNA data will confirm the epigenetic events changing important agronomical traits.
Project Planning
Since we are dedicated to provide the best bioinformatics data analysis we are interested to be involved in the project from the very beginning – if possible already during the proposal development to be able to accurately plan and follow the planting, sampling, sample preparation, DNA/RNA isolation, sequencing and data analysis and interpretation.
Capacity Building
Bioinformatics is a young discipline in Africa and we are aiming in teaching and training scientists and students. We are offering courses in bioinformatics at different levels, teaching and places in the lab for MS and and PhD students.
Transcriptomics
One of our major activities is RNA sequencing data analysis (total RNA and small non-coding RNA) to recover and discover transcripts from your sequenced samples but also calculate the expression levels and corresponding up and down regulation between different experimental conditions.
Within the projects we are part of, we are following the planting in the field, the sampling and harvesting.
Sampling for transcriptomics require a fast processing of the samples (leave, flower, stem and root) and a preservation in liquid nitrogen on the field.
Samples are processed by ourselves and high quality total RNA as well as small RNA are isolated for sending to the sequencing center. We have our preferred sequencing providers where we can expect high quality and fast sequencing.
