pedrorvc
Pedro Vila-Cerqueira • Mário Ramirez Lab
Bioinformatic Open Days 2020
Patient A
Patient B
Gene-by-Gene Based Typing Methods
Multilocus Sequence Typing (MLST)
PCR & Sanger Sequecing
Whole Genome Shotgun Sequencing
Gene-by-Gene Based Typing Methods
chewBBACA
https://github.com/B-UMMI/chewBBACA
File | Locus 1 | Locus 2 |
---|---|---|
genome1.fasta | Allele 2 | Allele 5 |
genome2.fasta | Allele 6 | Allele 9 |
chewBBACA
https://online.phyloviz.net
Core-Genome Multilocus Sequence Typing (cgMLST)
Is there an outbreak?
Strict privacy laws may prevent the users from sharing raw data. Unpublished data is also a matter of concern.
Schemas can be created with different parameters, requiring the users to share their configurations.
Profiles are generated based on the schema, which may contain private data, making it hard to share and obtain the same results.
What data to share?
Chewie-NS: a nomenclature server
Chewie-NS: a nomenclature server
Chewie-NS: a nomenclature server
NGINX:
Gunicorn:
Virtuoso Triple Store:
TypOn:
Git, Docker and Docker-compose to run multi-container Docker applications.
apt-get install git
apt-install docker-ce
curl -L "https://github.com/docker/compose/releases/download/1.25.3/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
git clone https://github.com/B-UMMI/Chewie-NS.git
Clone the repo
Deploy Chewie-NS
docker-compose up
Docker Compose
Chewie-NS: a nomenclature server
Chewie-NS: a nomenclature server
Chewie-NS: a nomenclature server
Chewie-NS: a nomenclature server
https://github.com/B-UMMI/Chewie-NS
Special thanks to Rafael Mamede, Inês Mendes, Mickael Silva, João André Carriço and Mário Ramirez.
https://github.com/B-UMMI/chewBBACA
This work was partially supported by the following projects: the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI – ‘Fundos Europeus Estruturais e de Investimento’ from ‘Programa Operacional Regional Lisboa 2020’ and by national funds from FCT – ‘Fundação para a Ciência e a Tecnologia’, BacGenTrack (TUBITAK/0004/2014) [FCT/Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBİTAK)] and LISBOA-01-0145-FEDER-007391, project cofunded by FEDER, through POR Lisboa 2020 - Programa Operacional Regional de Lisboa, PORTUGAL 2020, and Fundação para a Ciência e a Tecnologia.
Thank you for your attention!
https://github.com/B-UMMI/Chewie-NS_tutorial