index.rst

Course on Unix and work with genomic data - Prague, October 2024

This course takes place regularly in the winter term at the Department of Zoology, Faculty of Science, Charles University in Prague (MB170C47).

The aim of the course is to introduce the participants to Unix - an interface that is one of the most convenient options for working with big data in text formats. Special attention is given to working with Next Generation Sequencing (NGS) data. Most of the NGS data formats are intentionally text-based because the authors wanted to use Unix for most of the processing. Like that they can focus on the real problem they're solving without having to program special tools for the mundane tasks, which can all be handled by combining basic Unix tools.

We'll be using Slack 'UNIX and NGS' to share your login credentials and further info - use (this link to join).

Schedule:

Friday 11.10.2024 (14.00-18.00)
Afternoon	Course Intro Introduction to Unix Basics of Unix
Saturday 12.10.2024 (9.00-18.00)
Morning	Genomics data Processing of plain text files in Unix
Lunch Break (1.5h)
Afternoon	Running a project in Unix Graphics Session
Sunday 13.10.2024 (9.00-18.00)
Morning	Introduction to Git Variant quality exercise
Lunch Break (1.5h)
Afternoon	Bioinformatic pipelines Working remotely in the cloud

Initial instructions:

.. toctree::
   :maxdepth: 1

   install
   connect

Course outline:

.. toctree::
   :maxdepth: 2

   01-starter
   02-genomics
   03-file-processing
   04-project-management
   05-graphics
   07-git
   08-var-quality
   09-bioinfo-pipeline

Additional reference materials:

.. toctree::
   :maxdepth: 1

   links
   more-tips
   reference
   formats
   more-exercise

Supplemental information:

.. toctree::
   :maxdepth: 1

   prepare
   slides