Recap of WGS Workflow: Isolate to Analysis Day 3 Bioinformatics
Explore the recap of Day 3 covering bioinformatics, BIGSdb, Enterobase, and protocols. Dive into topics like FASTQ, assembly, mapping, and more. Engage in live exercises and lectures for a comprehensive learning experience on 26th March 2021.
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Presentation Transcript
WGS workflow: from isolate to analysis Day 3 Recap Bioinformatics, BIGSdb, Enterobase and protocols 26 March 2021 Pernille Nilsson
Virtual Housekeeping Please turn off your cameras and microphones this will help with bandwidth and maximise audibility. Do frequently use Slack to share comments and ask questions. Keep the chat constructive, respectful and on topic! For Q&A s use Slack to submit your questions! Please upvote (give a thumbs-up) to the questions that you like. The session is being recorded for distribution to participants as a post course resource as well as for future iterations of the course.
Day 3: Friday 26 March Recap Bioinformatics, BIGSdb, EnteroBase and protocols Link to Teams/Zoom/Platform Joining the call Assistance will be provided at this time to help participants join 09.00 09.15 Welcome and Introduction (Live) [7] Recap on bioinformatics: FASTQ, fasta; assembly, mapping, kmer counting, and why do we do it? (Pre-recorded) [8] Recap on CGE tools: Refreshing the knowledge on available online tools (Pre-recorded) 10.15 10.30 BREAK [9] Introduction to BIGSdb and EnteroBase: Demonstration of data analysis at EnteroBase (Pre-recorded) [9E] Exercise: Introduction to an exercise using EnteroBase. (Live) BREAK 08.45 09.00 Agenda Friday 26nd March 09:00 12.45 Marco van Zwetselaar (KCRI, Tanzania) 09.15 09.45 Marco van Zwetselaar (KCRI, Tanzania) 09.45 10.15 Lectures Anthony Smith (NICD, South Africa) 10.30 11.30 Anthony Smith (NICD, South Africa) 11.30 11.45 Exercises 11.45 12.00 Jette Sejer Kjeldgaard (DTU, Denmark) SurveyMonkey 12.00 12.30 [10] Protocols and ISOs: (Live) Errol Strain (FDA, USA) 12.30 -12.45 Q&A and Wrap-up (Live) 26 March 2021 The Fleming Fund | SEQAFRICA 3
[7] Recap on bioinformatics Marco van Zwetselaar (KCRI, Tanzania) ATC GAT 26 March 2021 The Fleming Fund | SEQAFRICA 4
[8] Recap on CGE tools Marco van Zwetselaar (KCRI, Tanzania) ATC GAT 26 March 2021 The Fleming Fund | SEQAFRICA 5
BREAK 10:40 -10:55 CET
[9] Introduction to BIGSdb and Enterobase Anthony Smith (NICD, South Africa) ATC GAT 26 March 2021 The Fleming Fund | SEQAFRICA 7
[9E] Exercise: Using Enterobase Anthony Smith (NICD, South Africa) ATC GAT 26 March 2021 The Fleming Fund | SEQAFRICA 8
BREAK 12:05 -12:15 CET
[10] Protocols and ISOs Jette Sejer Kjeldgaard (DTU, Denmark) Errol Strain (FDA, USA) ATC GAT 26 March 2021 The Fleming Fund | SEQAFRICA 10
Day 4: Monday 29 March Data sharing Link to Teams/Zoom/Platform Joining the call Assistance will be provided at this time to help participants join 08.45 09.00 Agenda Monday 29th March 09:00 11:15 09.00 09.15 Welcome and Introduction (Live) [11] Data sharing practices and repositories: Introducing how and where to make raw sequencing data and assembled genomes publicly available. GenBank (NCBI, ENA, Enterobase etc.) (Pre-recorded Lecture). Tolbert Sonda/Marco van Zwetselaar (KCRI, Tanzania) & Ayorinde Afolayan (UI, Nigeria) 09.15 10.15 BREAK 10.15 10.30 Shannon Williams (NICD, South Africa) Beverly Egyir (NMIMR, Ghana) Pernille Nilsson (DTU, Denmark) Anthony Smith (NICD, South Africa) 10.30 11.00 Going through results from all exercises (Live) 11.00 11.30 Q&A and Wrap-up (Live) 11.30 11.45 Concluding remarks and close (Live) 26 March 2021 The Fleming Fund | SEQAFRICA 12
Contact us for more information seqafrica@food.dtu.dk pnil@food.dtu.dk (Pernille Nilsson, Project Manager) rshe@food.dtu.dk (Rene S. Hendriksen, Technical Lead) antimicrobialresistance.dk/seqafrica.aspx @AfricaSeq 26 March 2021 The Fleming Fund | SEQAFRICA 13
Thank you This programme is being funded by the UK Department of Health and Social Care. The views expressed do not necessarily reflect the UK Government s official policies.
