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A brief introduction to the core concepts of the command line as a good environment for bioinformatics analysis. A hands-on tutorial to log in into a remote Linux server using each participant's laptop, and test the first commands. Our main goal is the setup of your clients, in order to allow you off-site access to the workshop!
- What is a terminal: the "terminal prompt"
- Accessing a remote server using ssh (Mac or Linux) or the program PuTTY (from Windows)
- Using
screen
to set up a persistent session on a remote server - The filesystem: using
pwd
andls
to interact with it from the terminal. Tab completion. -
mkdir
to create directories - A command-line text editor:
nano
Understanding the "file system", relative and absolute paths, and the commands to organize the directories, to list files, to copy and move files and directories. Introduction to commands to interact with text files and view them. We will use the FASTA and FASTQ file formats as examples.
-
ls
(with some parameters), wildcards,cd
,rmdir
,find
- Interactive visualization of text files:
less
- Viewing text files with
cat
,head
andtail
- Counting lines and characters with
wc
- Selecting lines with patterns using
grep
- Redirecting a command output into a text file
Using terminal commands to interact with bioinformatics files. We'll introduce the SAM file format used to store NGS mapping, the VCF format (for SNP calling), and some tabular annotation files (GFF, GTF).
- Recap of previous commands to be used with for SAM files
- Downloading datasets with wget
- The
sort
,uniq
,cut
commands - Joining tabular datasets with
join
- Command pipes: combining multiple commands
- Installing Miniconda to manage packages in your Linux / Mac
- The FASTA and FASTQ formats
- Common manipulations, conversions and statistics of sequence files
- Quality filtering and QC using
fastp
Using short reads alignment as a theme, we'll introduce how to install new software to be used from the command line, users and file permissions, and of course the alignment program bwa and samtools the swiss army knife to manipulate SAM files.
- Introduction to the SAM/BAM formats
- Using
bwa
to align short reads - Using
samtools
to operate with SAM/BAM files - Introduction to version-controlled repositories and
git
· Bioinformatics at the Command Line - Andrea Telatin, 2017-2020
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