• Alumni

Bernardo Clavijo

Group Leader - Bioinformatic Algorithms

Bernardo Clavijo

Biography.

A systems engineer from Argentina, Bernardo focused his teams research on Algorithm Development and Genome Assembly for NGS data. He is a proficient C/C++/Python programmer, somewhat of a Unix hacker, and loves HPC programming and performance tuning.

Involved in the IT industry for more than 10 years he worked as an analyst, programmer and distributed Unix systems consultant for banks, airlines, and government agencies. At INTA, Argentina, he participated in the international effort towards wheat genome sequencing and assembly, among other plant genomics and transcriptomics projects.

Bernardo’s team assembled and validated complex genomes using information and kmer based metrics. They developed the WGS/Wheat Robust Assembly Pipeline (w2rap), which produced the most comprehensive and precise wheat genome assembly by a public initiative to date and led the wheat community into the pan-genomic era, and worked on synteny-based alignment and comparison tools and multi-reference genomics.

KAT

The K-mer Analysis Toolkit, a tool to analyse k-mer spectra of NGS datasets and assemblies. Highly recommended for fast and simple at-a-glance QC of genome assembly content inclusion from Illumina datasets.

http://github.com/TGAC/KAT

w2rap

The assembly pipeline that is routinely and robustly delivering crop genomes from cost-effective short-read data.

http://github.com/bioinfologics/w2rap

w2rap-contigger

The contigger part of our assembly pipeline, forked from DISCOVAR denovo and improved to better handle complex and repetitive genomes, with more flexible parameters and improved results representation including standard graph outputs.

http://github.com/bioinfologics/w2rap-contigger

Triticum aestivum CS42 assembly and annotation

The wheat reference assembly described on our Genome Research publication, produced by our w2rap open method

http://opendata.earlham.ac.uk/Triticum_aestivum/TGAC/v1/

5 more wheat genomes (pre-publication access)

W2rap based assemblies of 4 hexaploids and 1 tetraploid wheat genomes. Open access under Toronto Agreement conditions.

http://opendata.earlham.ac.uk/Triticum_aestivum/EI/v1.1/

http://opendata.earlham.ac.uk/Triticum_turgidum/EI/v1.1/

Publications.

Related reading.