Bioinformatician / Bioinformatics analyst consultant
Specialties: NGS data analysis .
More than 5 years experience in programming and creation of bioinformatics tools.
Strong background with unix/linux tools and administration.
Strong programming skills in Unix based scripting language (Perl, Python etc.)
Strong coding skills with general purpose software development languages such as Java and C++.
Extended experience with mathematics and statistics packages such as Bioconductor and R.
Experience with High Throughput computing (Torque ,SGE).
Experience with MongoDB and with relational databases (MySQL)
A solid background in statistics, probability, pharmacogenomics , genetics and cancer genetics.
Experience with the Illumina HiSeq and MiSeq, Life Technologies Ion Torrent Ion Proton and with different genotyping platforms.
Solid and relevant experience in developing NGS data analysis pipelines including basecalling ,demultiplexing , mapping and variant calling .
Experience with large genomic (genome-wide array and next generation sequencing) datasets and relevant databases (e.g., Gene Ontology, UCSC Genome Bioinformatics)
Extensive experience with de novo genome assembly .
Familiar with NGS data analysis tools such as aligners (e.g., Bowtie, BWA, NovoAlign and MEM), quality control (e.g, Picard, FastQC, FASTX,GATK) ,SNP detection (e.g., SAMtools, GATK, Dindel,Pindel) and SNP annotation (Annovar ,Polyphen ,Panther ,SIFT ,LRT ,MT ,PhyloP ,Pmut ,SNPs3D).
Bachelor degree in biotechnologie
Past & ongoing projects:
-Perform initial stage analysis on next-generation sequencing data transforming data from sequence to information meaningful for biologists.
-Responsible for executing multiple bioinformatics priorities for the lab or core facility
-Provide input and guidance to trainees, lab staff, or scientists to advance research or project objectives.
-Communicate results and findings of analyses to investigators
-Use and develop analysis pipelines using in-house and 3rd party tools or algorithms : DNA-Seq , RNA-seq ,ChiP-seq, de novo assembly ...
-Write scripts/programs for bioinformatic tasks (e.g., sequence annotation and variant calling)
-Access and analyze large repositories of data through scripting procedures.
-Query and maintain database for genomic information e.g. https://www.pmgenomics.ca/bis/
-Leverage high performance computing service by writing scripts for large jobs
-Ensure the production LIMS, , and other production information systems are operational and meeting the day to day needs of the research laboratory team.
-Document and manage tasks employing good programming practices in commenting code, minimizing errors, and maximize efficiency (e.g., reusability of code).