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1. General guides
Introduction to the command line
Windows Subsystem for Linux
Using Ubuntu through a Virtual Machine
File formats used in bioinformatics
2. Program guides
Augustus
BLAST
Bcftools
Bowtie
Bowtie2
Conda
Fasterq-dump
Fastq-dump
FeatureCounts
Htseq-count
OrthoFinder
SAMtools
SPAdes
sgRNAcas9
3. Scripts
Annotated SNPs filter
Annotating SNPs
Combining featCount tables.py
DE analysis edgeR script.R
Fastq-dump to featureCounts
Genome annotation script
Linux setup script
SNP calling script
UniProt downloader
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Bioinformatics Notebook on GitHub
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If there are any errors or mistakes, please let me know.