The 2023 course will introduce the participants to the UNIX OS and Bash scripting along with a suite of bioinformatics tools covering the following topics:
▪ HTS sequencing technologies: overview of the different HTS platforms and sample preparations
▪ Unix OS: introduction to Unix OS and essential Bash scripting
▪ Reference assembly: aligning sequence reads to a known reference and visualization (e.g., bowtie2, BWA, Tanoti, Tablet, UGENE)
▪ Variant calling: consensus sequence generation, low frequency variant calling and error correction (e.g., samtools, LoFreq, DiversiTools)
▪ De-novo assembly: overlap layout and de Bruijn graphs approaches for sequence assembly, quality assessment and merging contigs (e.g., ABySS, SPAdes, MIRA, IDBA-UD, QUAST)
▪ Metagenomic analyses:sanitizing sequence datasets, assembling, annotating, visualization (e.g., MetAMOS, Krona, DIAMOND, Kraken)
▪ Genomics: scaffolding, improving and finishing the assembly, gene annotation (e.g., ICORN, Artemis, RATT)
▪ Phylogenetic analysis: introduction to multiple sequence alignment and phylogenetic reconstruction (e.g., Muscle, PhyML, FigTree)
Preference will be given to applicants who: (1) have some familiarity with HTS technologies; (2) have already or are planning to generate viral HTS data in their work; and (3) have an interest in computers and programming (some basic experience in a command-line environment is a prerequisite)
David Robertson
Derek Wright
Joseph Hughes (Course Organizer)
Quan Gu
Richard Orton
Sreenu Vattipally
Srikeerthana Kuchi (Course Organizer)