2026 | Santiago, Chile
Day 1
| Time | Activity | Speaker |
|---|---|---|
| 08:30-09:00 | • Registration | |
| 09:00-10:00 | • Welcome remarks • Participants’ introductions • Objectives of the training • Group photo |
US CDC - Davis|Dugan? All participants US CDC All participants |
| 10:00-10:30 | Tea/coffee break | |
| 10:30-12:30 | Lecture #1: VSDB overview | Davis|Kondor, US CDC |
| 12:30-13:30 | Lunch break | |
| 13:30-14:30 | Computer basics • OS (linux v mac v windows) • Overview of scripting languages • Ssh (working on servers/remotes) • Parallelization (multiple cpus / multiple nodes) –threads |
US CDC |
| 14:30-15:00 | Tea/coffee break | |
| 15:00-15:30 | Computer basics • Ssh (working on servers/remotes) • Parallelization (multiple cpus / multiple nodes) –threads |
US CDC |
| 15:30-16:30 | Computer setup (WSL) | US CDC |
| 16:30-16:45 | Wrap-up |
Day 2
| Time | Activity | Speaker |
|---|---|---|
| 09:00-10:00 | Identify individual needs • Discuss each participants surveillance network • Discuss questions that can be answered with genomic data |
US CDC |
| 10:00-10:15 | Tea/coffee break | |
| 10:15-11:30 | Intro to Command Line Interface (CLI) • Practical using shell commands to download spreadsheet of sample metadata and manipulate/summarize. • Cd, ls, mkdir, curl, head, tail, sed, grep, piping, regex… |
US CDC |
| 11:30-12:00 | NGS filetypes presentation | US CDC |
| 12:00-13:00 | Lunch break | |
| 13:00-14:30 | Fastq manipulation • Download test data • Tar and gzip compression • Rename files using samplesheet • Summary stats with samtools • Trimming? • Demux? |
US CDC |
| 14:30-15:00 | Tea/coffee break | |
| 15:00-15:15 | Containers and registries • Docker • podman |
|
| 15:15-16:30 | MIRA review and run test data | US CDC |
| 16:30-16:45 | Q&A |
Day 3
| Time | Activity | Speaker |
|---|---|---|
| 08:30-9:00 | Daily Overview | US CDC |
| 9:00-9:30 | Fasta manipulation with bash • Prepare seqsender fasta and metadata files |
|
| 9:30-10:30 | Seqsender practical | |
| 10:30-11:00 | Tea/coffee break | |
| 11:00-11:30 | Blast • NCBI • GISAID • Build your own |
|
| 11:30-12:00 | Lecture – sequence alignment algorithms • Global vs. local |
|
| 12:00-13:00 | Lunch break | |
| 13:00-16:30 | Identifying genetic markers • Glycosylation • NAI • Mammalian adaptation • Limitations |
|
| 16:30-16:45 | Q&A |
Day 4
| Time | Activity | Speaker |
|---|---|---|
| 08:30-10:00 | Phylogenetics day! | |
| 10:00-10:30 | Tea/coffee break | |
| 10:30-12:00 | • Quality Management Systems for Bioinformatics | |
| 12:00-13:00 | Lunch break | |
| 13:00-16:00 | • | |
| 16:00-16:30 | Q&A |
Day 5
| Time | Activity | Speaker |
|---|---|---|
| 08:30-10:00 | Troubleshooting Lab • Low Ct • Poor PCR • Index swapping • Contamination vs. Co-infection • Controls |
US CDC |
| 10:00-10:30 | Tea/coffee break | |
| 10:30-12:00 | Troubleshooting Bioinformatics • Shell environment • Invisible characters & encoding • Dos2unix • Linux permissions • Sequence quality • Reference filling • LAIV • Missing sequence |
US CDC |
| 12:00-13:00 | Lunch break | |
| 13:00-13:30 | Workflow pipelines • Snakemake • Nextflow • WDL |
US CDC |
| 13:30-15:00 | Databases • Defining requirements • Authentication • Concurrency • Backups • Physical access • Data model • Reporting/analytics • SQL practical |
US CDC |
| 15:00-15:30 | 3d modeling, metagenomics, AI, bioinformatics outlook discussion | |
| 15:00-15:30 | Closing remarks, Certificates of Completion, Tea/coffee | US CDC |