Canadian Centre for Computational Genomics

Mentors: Student: Andjela Todorovic

<p>The objective of the problem arises from the reconstruction of gene genealogies problem - from a given genotypes of sequence data from contemporary individuals and an extended pedigree of genealogical relationships among them we have to decide and be very clear about what we should consider to be nodes information in genealogy tree according to kinds of dependencies among these nodes which should be considered to be edges of the tree. This project will focus on the development of novel algorithms for advanced reconstruction of the gene genealogy by performing inference on graphical models, specifically, implementing the greedy approach and loopy belief propagation algorithm on the succinct tree sequences. The implemented algorithms would undoubtedly be of use to integrate into the existing tskit and msprime libraries.</p>

Mentors: Student: Harshit Maheshwari

<p>The Canadian Common CV (CCV) is a tool that allows Canadian researchers to input their resume in a standardized format. It is used by multiple organizations such as granting agencies, federal, provincial and academic institutions. The tool enables users to output results in an XML document, that can be used in external applications.</p> <p>The main objective is to build an application that can ingest, store and query data from the CCV and show the results in a dashboard. The Web Application will be developed in line with a well documented, tested feature list, able to work across on all browsers.</p>

Mentors: Student: Mohd Arshul Mansoori

<p>DevOps for GenPipes would create an automatic deployment of the GenPipes project in the cloud using Terraform. It would support multiple cloud platforms such as AWS, GCP, OpenStack Cloud etc.</p>

Mentors: Student: Moonshroom

<p>GenPipes is an important tool by C3G. GenPipes contains a suite of different software. The software contained in the suite is continuously updated but there is no method as of now to automatically update the software catalog which is available on the C3G Website. The goal of the project is to develop a pipeline to automate the updating of the software stack, while also adding some more metadata which would be relevant to the software.</p>

Mentors: Student: Konstantinos Kyriakidis

<p>The majority of contemporary genomics and transcriptomics research is carried out using short-read technology such as the output of Illumina sequencers. However, newer long-read technologies such as PacBio and Oxford Nanopore (ONT) are becoming more prevalent due to the advantages they offer over short reads. The main advantage of long reads is that they span a much larger portion of the genome or transcriptome, making it easier to detect events such as structural variants or isoforms. As more researchers begin to take advantage of long reads, GenPipes needs to evolve and support long-read technology in its main pipelines. The objective of this project is to create a new RNA-seq pipeline (rnaseq_longreads), that supports long-read inputs. The new pipeline will be created based on the current versions of the RNA-seq pipeline, with the addition of the minimap2 aligner as well as StringTie v2 and Ballgown for generating transcript counts. In addition to implementing a long-read RNA-seq pipeline within the GenPipes framework, short-read RNA-seq pipeline will also be updated to utilize StringTie2 and both pipelines will be tested to ensure that they are working properly.</p>