2nd Viral Bioinformatics and Genomics Training Course (1st – 5th August 2016)

• Post by: Joseph Hughes
• August 10, 2016
• 3 Comments

We have shared our knowledge on Viral bioinformatics and genomics with yet another clever and friendly bunch of researchers. Sixteen delegates from across the world joined us for a week of intensive training. The line-up of instructors changed slightly due to the departure of Gavin Wilkie earlier in the year.

Instructors:
Joseph Hughes (Course Organiser)
Andrew Davison
Sejal Modha
Richard Orton (co-organiser)
Sreenu Vattipally
Ana Da Silva Filipe

The timetable changed a bit with more focus on advanced bash scripting (loops and conditions) as we asked the participants to have basic linux command experience (ls, mkdir, cp) which saved us a lot of time. Rick Smith-Unna’s Linux bootcamp was really useful for the students to check their expertise before the course: http://rik.smith-unna.com/command_line_bootcamp.

The timetable this year follows and as in the previous year, we had plenty of time for discussion at lunch time and tea breaks and the traditional celebratory cake at the end of the week.

9:00-9:45                 Tea & Coffee in the Barn – Arrival of participants

DAY 1 – SEQUENCING TECHNOLOGIES AND A UNIX PRIMER

The first day will start with an introduction to the various high-throughput sequencing (HTS) technologies available and the ways in which samples are prepared, with an emphasis on how this impacts the bioinformatic analyses. The rest of the first day and the second day will aim to familiarize participants with the command line and useful UNIX commands, in order to empower them to automate various analyses.

9:45-10:00           Welcome and introductions – Massimo Palmarini and Joseph Hughes

10:00-10:45        Next-generation sequencing technologies – Ana Da Silva Filipe

10:45-11:15        Examples of HTS data being used in virology – Richard Orton
11:15:11:30            Short break
11:30-11:45        Introduction to Linux and getting started – Sreenu Vattipally

11:45-12:30        Basic commands – Sreenu Vattipally
12:30-13:30            Lunch break in the Barn followed by a guided tour of the sequencing facility with Ana Da Silva Filipe
13:30-14:30        File editing in Linux – Sreenu Vattipally & Richard Orton
14:30-15:30        Text processing – Sreenu Vattipally & Richard Orton
15:30-16:00            Tea & Coffee in the Barn Room
16:00-17:30        Advanced Linux commands – Sreenu Vattipally
DAY 2 – UNIX CONTINUED AND HOW TO DO REFERENCE ASSEMBLIES

The second day will continue with practicing UNIX commands and learning how to run basic bioinformatic tools. By the end, participants will be able to analyse HTS data using various reference assemblers and will be able to automate the processing of multiple files.

9:30-11:00           BASH scripting (conditions and loops) – Sreenu Vattipally
11:00-11:30            Tea & Coffee in the Barn Room
11:30-12:15        Introduction to file formats (fasta, fastq, SAM, BAM, vcf) – Sreenu Vattipally & Richard Orton
12:15-13:00        Sequence quality checks – Sreenu Vattipally & Richard Orton
13:00-14:00            Lunch break in the Barn followed by a guided tour of the sequencing facility with Ana Da Silva Filipe
14:00-14:45        Introduction to assembly (BWA and Bowtie2)– Sreenu Vattipally & Richard Orton
14:45-15:30        More reference assembly (Novoalign, Tanoti and comparison of mapping methods) – Sreenu Vattipally & Sejal Modha
15:30-16:00            Tea & Coffee in the Barn Room
16:00-17:30        Post-processing of assemblies and visualization (working with Tablet and Ugene and consensus sequence generation) – Sreenu Vattipally & Sejal Modha
DAY 3 – HOW TO DO VARIANT CALLING AND DE NOVO ASSEMBLY

The third day will start with participants looking at variant calling and quasi-species characterisation. In the afternoon, we will use different approaches for de novo assembly and also provide hands-on experience.

9:30-11:00           Error detection and variant calling – Richard Orton

11:00-11:30            Tea & Coffee in Barn Room
11:30-13:00        Quasi-species characterisation – Richard Orton
13:00-14:00            Lunch break in the Lomond Room with an informal presentation of Pablo Murcia’s research program.

14:00-14:45        De novo assemblers – Sejal Modha
14:45-1:30           Using different de novo assemblers (e.g. idba-ud, MIRA, Abyss, Spades) – Sejal Modha
15:30-16:00            Tea & Coffee in the Barn
16:00-17:30        Assembly quality assessment, merging contigs, filling gaps in assemblies and correcting errors (e.g. QUAST, GARM, scaffold builder, ICORN2, spades) – Sejal Modha
DAY 4 – METAGENOMICS AND HOW TO DO GENOME ANNOTATION

On the fourth day, participants will look at their own assemblies in more detail, and will learn how to create a finished genome with gene annotations. A popular metagenomic pipeline will be presented, and participants will learn how to use it. In the afternoon, the participants will build their own metagenomic pipeline putting in practice the bash scripting learnt during the first two days.

9:30-10:15           Finishing and annotating genomes – Andrew Davison & Sejal Modha
10:15-11:00        Annotation transfer from related species – Joseph Hughes
11:00-11:30            Tea & Coffee in the Barn
11:30-12:15        The MetAMOS metagenomic pipeline – Sejal Modha & Sreenu Vattipally
13:00-14:00            Lunch break in Lomond Room with informal presentation of Roman Biek’s research program.

14:00-15:30        Practice in building a custom de novo pipeline – Sejal Modha & Sreenu Vattipally

15:30-16:00            Tea & Coffee in the Barn
16:00-17:30        Practice in building a custom de novo pipeline – Sejal Modha

17:30                         Group photo followed by social evening and Dinner at the Curler’s Rest (http://www.thecurlersrestglasgow.co.uk). 

DAY 5 – PRIMER IN APPLIED PHYLOGNETICS

On the final day, participants will combine the the consensus sequences generated during day two with data from Genbank to produce phylogenies. The practical aspects of automating phylogenetic analyses will be emphasised to reinforce the bash scripting learnt over the previous days.

9:30-10:15           Downloading data from GenBank using the command line – Joseph Hughes & Sejal Modha
10:15-11:00        Introduction to multiple sequence alignments – Joseph Hughes
11:00-11:30            Tea & Coffee in the Barn
11:30-1300         Introduction to phylogenetic analysis – Joseph Hughes
13:00-14:00            Lunch break in the Lomond Room with a celebratory cake

14:00-15:30        Analysing your own data or developing your own pipeline – Whole team available
15:30-16:00            Tea & Coffee in the Barn
16:00-17:00        Analysing your own data or developing your own pipeline – Whole team available
17:00                       Goodbyes
We wish all the participants lots of fun with their new bioinformatic skills.

If you are interested in finding out about future course that we will be running, please fill in the form with your details.