/adv_binf_2023_week1

Teaching material used in the "Advanced Bioinformatics for Next-Generation Sequencing" class, University of Copenhagen, 2023

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Advanced Bioinformatics for Next-Generation Sequencing 2022: Week 1

Day Time Subject Lecturer
Day 1 - Monday 9:15 - 12 NGS data - Workflow, formats and programs Thorfinn Sand Korneliussen
Day 2 - Tuesday 13:15 - 16 Mapping - Suffix arrays and Burrows-Wheeler Transform Rasmus A. Henriksen
Day 3 - Friday 9:15 - 12 K-mers and metagenomic sequence classification Abigail Ramsøe

Getting started

Connecting to the server via SSH

X11 forwarding method will allow you to start a graphical application on the remote system and forward this application's windows to your local system. We need to enable X11 forwarding to view the plots we will be generating for the exercises.

We use -X option to enable X11 forwarding over SSH:

$ ssh -X <your_username>@<server_name_or_ip>

Replace with your remote server username. For example:

$ ssh -X isin@emily.popgen.dk

Setting up the working environment

If you are working on the emily server, all commands in the following seven exercises will be relative to the base directory called /TEACHING/BIOINF23/adv_binf_2023_week1

day1
├── data
│   ├── alignment
│   ├── fasta
│   ├── fastq
│   ├── reference_fasta
│   └── reference_fasta_hs37d5
├── exercises
│   ├── alignment_formats
│   ├── mapdamage
│   ├── trimming
│   └── variant_call_format
├── Makefile
└── README.md