EpiCass & CassavaNet4DevSecond Advanced Bioinformatics Workshop15 - 19 May 2023EndFragment

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EpiCass: Identification of epigenetic variations influencing viral resistance and yield in cassava (Manihot esculenta) farmers’ fields CASSAVANET4DEV: In a race to prevent hunger: Cassava Bioinformatics for African cassava biotechnology. Research on plant epigenetics helps to understand how endogenous, biotic, and abiotic factors might regulate plant growth, development, and interaction with the environment independent of changes in the genome sequence. Often, the epigenetic changes are heritable across several generations and harmonize plant growth and crop tolerance in response to environmental stimuli.To take advantage of the knowledge of the epigenetic adaptation, it has the potential to provide a powerful toolbox for crop breeders; however, most mechanistic studies are based on information from model plant species due to the challenges that arise when working with crops in the field. EpiCass and CassavaNet4Dev are projects financed by the Swedish Research Council that will aim to sequence different field grown cassava genotypes under different conditions to study the DNA methylation profiles and potential methylation pattern related to ACMV resistance and yield variation in farmer’s fields and disseminate the technology, data acquired, knowledge gained as well as train African scientists in bioinformatics to learn how to analyze such data by including them in our data analysis efforts. We organize a second advanced bioinformatics workshop at IITA Hubs in Nairobi and Ibadan as well as at BETin in Addis Ababa. The course will be run in a hybrid on-line and in-person approach in parallel sessions between the three locations, training students and researchers from any institutions close to the venues in NGS data analysis. EndFragment

The course is for students and researchers who have demonstrable basic knowledge in bioinformatics.If you meet the criteria, please register via: https://bit.ly/366unAR Deadline for registration 21 April 2023. We will select the final participants according to their skills and projects they are involved, and we will inform you by 29 April 2023.EndFragment

Objectives of the course topics By the end of the course participants should be able to:●      Use Linux command-line as a tool for data analysis ●      Describe and differentiate the different NGS data file formats ●      Perform QC assessment on NGS data ●      Perform mapping and sequence assembly using NGS data●      Use Haplotype-resolved reference genomes for data analysis

Organizers:Prof. Erik Bongcam-Rudloff, SLU, Uppsala, Sweden Dr. Livia Stavolone IPSP-CNR, Bari, Italy Dr Laurent Falquet, UniFr, Switzerland Dr. Adnan Niazi, SLU, Uppsala, Sweden Trushar Shah, IITA, Nairobi, Kenya Renaud van Damme, SLU, Uppsala, Sweden Michael Landi, IITA, Nairobi, Kenya Dr. Andreas Gisel, ITB-CNR, Bari, Italy & IITA, Ibadan, CNR EndFragment

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Day Time (EAT)Time (CET)Time (WAT)Teacher 3Recap on Day 210:00 - 10:3009:00 – 09:3008:00 – 08:30Erik Bongcom-Rudloff, SLU Uppsala, Sweden   Introduction Epigenetics   10:30 - 11:2009:30 - 10:2008:30 - 09:20Livia Stavolone, IPSP-CNR, Italy   Coffee Break11:20 - 11:3010:20 – 10:3009:20 - 09:30  NGS Assembly - Introduction11:30 - 12:1010:30 - 11:1009:30 - 10:10Adnan Niazi, SLU Uppsala, Sweden NGS Assembly – Different approaches12:10 - 13:0011:10 - 12:0010:10 - 11:00Adnan Niazi, SLU Uppsala, Sweden Lunch Break13:00 - 14:3012:00 – 13:3011:00 – 12:30  Hands-on for assembly   14:30 – 18:00 13:30 – 17:00 12:30 – 16:00 Adnan Niazi, SLU Uppsala, Sweden Local teachers:[if !supportLists]·       [endif]Nairobi: Michael Landi [if !supportLists]·       [endif]Addis Ababa: Trushar Shah, [if !supportLists]·       [endif]Ibadan: Andreas Gisel EndFragment

Day Time (EAT)Time (CET)Time (WAT)Teacher 2Recap on Day 110:00 - 10:3009:00 – 09:3008:00 – 08:30Erik Bongcom-Rudloff, SLU Uppsala, Sweden Linux part 3 – Advanced Commands 10:30 - 11:0009:30 - 10:0008:30 - 09:00Michael Landi, IITA, Nairobi Hands-on for Linux11:00 – 11:3010:00 – 10:3009:00 – 09:30Local teachers:[if !supportLists]·       [endif]Nairobi: Michael Landi, [if !supportLists]·       [endif]Addis Ababa: Trushar Shah, [if !supportLists]·       [endif]Ibadan: Andreas Gisel Coffee Break11:30 - 11:5010:30 – 10:5009:30 - 09:50  Hands-on for Linux11:50 - 13:0010:50 - 12:0009:50 - 11:00Local teachers:[if !supportLists]·       [endif]Nairobi: Michael Landi, [if !supportLists]·       [endif]Addis Ababa: Trushar Shah, [if !supportLists]·       [endif]Ibadan: Andreas Gisel Lunch Break13:00 - 14:3012:00 – 13:3011:00 – 12:30  Introduction in UGENE14:30 – 15:0013:30 – 14:0012:30 – 13:00Erik Bongcam-Rudloff, SLU, Uppsala Hands-on for QC and mapping   15:00 – 18:00 14:00 – 17:00 13:00 – 16:00 Local teachers:[if !supportLists]·       [endif]Nairobi: Michael Landi [if !supportLists]·       [endif]Addis Ababa: Trushar Shah, [if !supportLists]·       [endif]Ibadan: Andreas Gisel EndFragment

Day Time (EAT)Time (CET)Time (WAT)Teacher 5Recap on Day 410:00 - 10:3009:00 – 09:3008:00 – 08:30Erik Bongcom-Rudloff, SLU Uppsala, Sweden Hands-on mapping on haplotype-resolved genome10:30 - 11:2009:30 - 10:2008:30 - 09:20Local teachers:[if !supportLists]·       [endif]Nairobi: Michael Landi [if !supportLists]·       [endif]Addis Ababa: Trushar Shah, [if !supportLists]·       [endif]Ibadan: Andreas Gisel Coffee Break11:20 - 11:3010:20 – 10:3009:20 - 09:30  Hands-on mapping on haplotype-resolved genome11:30 - 13:0010:30 – 12:0009:30 - 11:00Local teachers:[if !supportLists]·       [endif]Nairobi: Michael Landi [if !supportLists]·       [endif]Addis Ababa: Trushar Shah, [if !supportLists]·       [endif]Ibadan: Andreas Gisel Lunch Break13:00 - 14:3012:00 – 13:3011:00 – 12:30  Hands-on mapping on haplotype-resolved genome & analysis of the mapping14:30 – 18:00 13:30 – 17:00 12:30 – 16:00 Local teachers:[if !supportLists]·       [endif]Nairobi: Michael Landi [if !supportLists]·       [endif]Addis Ababa: Trushar Shah, [if !supportLists]·       [endif]Ibadan: Andreas Gisel EndFragment

Day Time (EAT)Time (CET)Time (WAT)Teacher 4Recap on Day 310:00 - 10:3009:00 – 09:3008:00 – 08:30Erik Bongcom-Rudloff, SLU Uppsala, Sweden Introduction in haplotye-resolved genome10:30 - 11:2009:30 - 10:2008:30 - 09:20Adnan Niazi, SLU Uppsala, Sweden Coffee Break11:20 - 11:3010:20 – 10:3009:20 - 09:30  Haplotype-resolved Cassava genome11:30 - 12:1010:30 - 11:1009:30 - 10:10Michael Landi, IITA, Nairobi Data analysis using haplotype-resolved genome: case cassava12:10 - 13:0011:10 - 12:0010:10 - 11:00Andreas Gisel, IITA, Nigeria & CNR-ITB, Italy Lunch Break13:00 - 14:3012:00 – 13:3011:00 – 12:30  The power of chromosome-scale, haplotype-resolved genomes 14:30 – 15:30 13:30 – 14:30 12:30 – 13:30 TBD  Presentation of another haplotype-resolved plant genome15:30 – 16:3014:30 – 15:3013:30 – 14:30 TBD EndFragment

Day Time (EAT)Time (CET)Time (WAT)Teacher 1Greetings10:00 - 10:3009:00 – 09:3008:00 – 08:30Erik Bongcom-Rudloff, SLU Uppsala, Sweden; coordinator EpiCass Lenna Tripati, IITA; Hub director Eastern Africa Michael Abberton, IITA; Hub director Western Africa Kassahun Tesfaye, BETin, Ethiopia;  Director General Introduction to NGS   10:30 - 11:2009:30 - 10:2008:30 - 09:20Laurent Falquet, University of Fribourg, Switzerland Coffee Break11:20 - 11:3010:20 – 10:3009:20 - 09:30  NGS Quality Control and file formats11:30 - 12:1010:20 - 11:1009:20 - 10:10Michael Landi, IITA, Nairobi NGS Mapping and file formats12:10 - 13:0011:10 - 12:0010:10 - 11:00Trushar Shah, IITA, Nairobi Lunch Break13:00 - 14:0012:00 – 13:0011:00 – 12:00  Linuxpart 1 - Introduction)14:00 – 14:4013:00 – 13:4012:00 – 12:40Erik Bongcam-Rudloff, SLU, Uppsala Linux part 2 – Basic Commands 14:40 – 15:0013:00 – 14:0012:40 – 13:00Renaud Van Damme, SLU Sweden   Hands-on for Linux15:00 – 18:00 14:00 – 17:00 13:00 – 16:00 Local teachers:[if !supportLists]·       [endif]Nairobi: Michael Landi, [if !supportLists]·       [endif]Addis Ababa: Trushar Shah, [if !supportLists]·       [endif]Ibadan: Andreas Gisel   EndFragment

EpiCass & CassavaNet4DevSecond Advanced Bioinformatics Workshop15 - 19 May 2023EndFragment

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EpiCass: Identification of epigenetic variations influencing viral resistance and yield in cassava (Manihot esculenta) farmers’ fieldsCASSAVANET4DEV: In a race to prevent hunger: Cassava Bioinformatics for African cassava biotechnology. Research on plant epigenetics helps to understand how endogenous, biotic, and abiotic factors might regulate plant growth, development, and interaction with the environment independent of changes in the genome sequence. Often, the epigenetic changes are heritable across several generations and harmonize plant growth and crop tolerance in response to environmental stimuli.To take advantage of the knowledge of the epigenetic adaptation, it has the potential to provide a powerful toolbox for crop breeders; however, most mechanistic studies are based on information from model plant species due to the challenges that arise when working with crops in the field. EpiCass and CassavaNet4Dev are projects financed by the Swedish Research Council that will aim to sequence different field grown cassava genotypes under different conditions to study the DNA methylation profiles and potential methylation pattern related to ACMV resistance and yield variation in farmer’s fields and disseminate the technology, data acquired, knowledge gained as well as train African scientists in bioinformatics to learn how to analyze such data by including them in our data analysis efforts.We organize a second advanced bioinformatics workshop at IITA Hubs in Nairobi and Ibadan as well as at BETin in Addis Ababa. The course will be run in a hybrid on-line and in-person approach in parallel sessions between the three locations, training students and researchers from any institutions close to the venues in NGS data analysis.Organizers: Prof. Erik Bongcam-Rudloff, SLU, Uppsala, Sweden Dr. Livia Stavolone IPSP-CNR, Bari, Italy Dr Laurent Falquet, UniFr, Switzerland Dr. Adnan Niazi, SLU, Uppsala, Sweden Trushar Shah, IITA, Nairobi, Kenya Renaud van Damme, SLU, Uppsala, Sweden Michael Landi, IITA, Nairobi, Kenya Dr. Andreas Gisel, ITB-CNR, Bari, Italy & IITA, Ibadan, CNR EndFragment

Objectives of the course topics By the end of the course participants should be able to:●      Use Linux command-line as a tool for data analysis ●      Describe and differentiate the different NGS data file formats ●      Perform QC assessment on NGS data ●      Perform mapping and sequence assembly using NGS data●      Use Haplotype-resolved reference genomes for data analysis

The course is for students and researchers who have demonstrable basic knowledge in bioinformatics.If you meet the criteria, please register via:https://bit.ly/366unARDeadline for registration 21 April 2023. We will select the final participants according to their skills and projects they are involved, and we will inform you by 29 April 2023.EndFragment

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