|
|
|
||
Last update: Ing. Jindřiška Peterková (12.09.2023)
We present an updated course with focus on remote computing and code reproducibility. Participants of the course will gain sufficient skills and confidence in unix-like environments in order to be able to use it for processing and analysis of their own genomics data. Besides a lot of hands-on exercise we will also provide an overview of available computational environments used in academic as well as commercial setups in bioinformatics. |
|
||
Last update: Mgr. Václav Janoušek, Ph.D. (15.09.2015)
I. Introduction to Unix - Learn about the Unix philosophy. II. Basic Unix - Learn to use the basic commands (cd, ls, ll, mkdir, mv, cp, pwd, htop, screen, grep, globbing, less, head, tail, cat, cut, sort, uniq, paste, join, pipes). III. Advanced Unix - Learn basics of awk, sed, regular expressions, shell scripting, shell variables, parallel, subshells. IV. Introduction to Genomics - Learn how ‘genomes’ are made. V. Data visualization - Learn how to format your data for effective visualization and how to use RStudio, tidyr, dplyr and ggplot2 to explore your data visually. VI. Read quality assessment - Learn how to use Unix to explore FASTQ files, calculate some basic statistics, assess read quality, filter out low-quality reads. VII. Genome assembly - Learn how to do a (small) genome assembly. VIII. Variant calling - Learn how to use the original NGS reads and a genome assembly to call variants. IX. Standard annotation formats - Learn how information on genes, variants and genome properties is stored (GFF, VCF, BED formats) and how to obtain quick summaries with impressive speed (bedtools, vcftools, etc.) X. A lot of practice. |