Reproducible genomics workflows using Nextflow and nf-core
17-20 November 2020
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All sessions will take place in Central European Standard Time (GMT+1)
TUESDAY 17th November 2020
TUESDAY 17th November 2020
Chair: Cedric Notredame (CRG)
9.30 - 9.45 - Welcome - Cedric Notredame | Centre for Genomic Regulation (CRG) - YouTube Streaming
9.45 - 10.30 - Introduction to Nextflow - Evan Floden | Sequera Labs - YouTube Streaming
10.30 - 11.20 - Nextflow training* (for accepted participants only)
11.20 - 11.30 - Break
11.30 - 12.30 - Nextflow training* (for accepted participants only)
12.30 - 13.00 - Flash talks - YouTube Streaming
From Snakemake to Nextflow - Daniel Fischer | Natural Resources Institute Finland (Luke)
Dynamics of direct transmission of Carbapenem resistance in Enterobacterales between human families and their companion animal - Juliana Menezes | Faculdade de Medicina Veterinária, Universidade de Lisboa *this talk will not be streamed
13.00 - 14.30 - Break
14.30 - 15.00 - HACKATHON: introduction and presentation of projects - Zoom Session
14.30 - 17.30 - HACKATHON - Zoom Session
WEDNESDAY 18th November 2020
WEDNESDAY 18th November 2020
Chair: Andreia Amaral
9.30 - 11.20 - Nextflow training* (for accepted participants only)
11.20 - 11.30 - Break
11.30 - 12.15 - Introduction to nf-core - Phil Ewels | SciLifeLab - YouTube Streaming
12.15 - 13.00 - Flash talks - YouTube Streaming
BOmA - Bovine Omics Atlas - Siddharth Jayaraman | The Roslin Institute
Structural variations in the cattle genomes - Bala Kiran Manthri | SLU University
Detection of Mobile genetic elements insertion sites in Swiss cattle breeds - Meenu Bhati | ETH, Zurich
GWA, mQTL and eQTL studies with imputed whole genome variants for BovReg traits - Praveen Krishna Chitneedi | Leibniz Institute for Farm Animal Biology (FBN)
13.00 - 14.30 - Break
14.30 - 15.00 - Hackathon advances from the previous day - Zoom Session
14.30 - 17.30 - HACKATHON - Zoom Session
THURSDAY 19th November 2020
THURSDAY 19th November 2020
Chair: Daniel Fischer
9.30 - 11.20 - Nextflow training* (for accepted participants)
11.20 - 11.30 - Break
11.30 - 12.30 - Featured nf-core pipelines - Harshil Patel | The Francis Crick Institute - YouTube Streaming
12.30 - 13.00 - Flash talks - YouTube Streaming
The evolution of the IsomiR Window, an upgrade to nextflow and nf-core - Andreia Amaral | Faculdade de Medicina Veterinária da Universidade de Lisboa
Functional and Structural Genomics Annotation - Gabriel Moreira | University of Liège
Large scale sequence level imputation for dairy industry - Tuan Nguyen | Agriculture Victoria
13.00 - 14.30 - Break
14.30 - 15.30 - Running nf-core pipelines + Contributing to nf-core - Phil Ewels | SciLifeLab - YouTube Streaming
15:30-15:40 Break
15.40 - 16.10 - Hackathon advances from the previous day - Zoom Session
16.00 - 17.30 - HACKATHON - Zoom Session
FRIDAY 20th November 2020
FRIDAY 20th November 2020
Chair: Jose Espinosa-Carrasco (CRG)
9.30 - 11.20 - Nextflow training* (for accepted participants)
11.20 - 11.30 - Break
11.30 - 12.30 - Introduction to DSL2 - Paolo di Tommaso | Seqera Labs - YouTube Streaming
12.30 - 13.00 - Flash talks - YouTube Streaming
Improving genome annotations with RNA-seq data: a new pipeline to combine transcript reconstruction and expression assessment - Cyril Kurylo | INRAE
Link-HD: a flexible tool to integrate and explore association between multiple microbial communities - Yuliaxis Ramayo Caldas | IRTA
GENE-SWitCH methylation pipeline for coherent methylation analysis - Jani de Vos | Wageningen University & Research
13.00 - 14.30 - Break
14.30 - 15.00 - Master of Pores: "A nanopore processing pipeline" - Luca Cozzuto | CRG - YouTube Streaming
15.00 - 17.00 - HACKATHON - Zoom Session
17.00 - 17.30 - Presentation of the HACKATHON projects and closing - Zoom Session
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