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| Terminal Basics beginner | Get up to speed with the terminal. Start here if you're new to bioinformatics. | |
| Wrangle FASTA and FASTQ with SeqKit beginner New | Explore and wrangle .fasta and .fastq files with SeqKit | |
| How to write a Bash script beginner New | How to turn your one-liners into reusable command-line scripts | |
| Terminal Exercises intermediate New | Command-line exercises from the Carpentries' Unix Shell lesson. |
| Bedtools tutorial beginner | Explore and wrangle .bed files with bedtools. | |
| IGV tutorial beginner | Distinguish real variants from artifacts using the IGV genome browser. | |
| DNA sequencing QC beginner | Evaluate the quality of a sequencing run by running fastp on your FASTQ files. | |
| BAM parsing with samtools beginner | Explore and wrangle .sam/.bam files with samtools. | |
| Sequence alignment with bowtie2 beginner | Align reads to a reference genome. | |
| BLAST tutorial beginner | Use BLAST to align DNA and protein sequences. | |
| K-mer counting with Jellyfish beginner | Learn the basics of k-mer counting using Jellyfish | |
| Aligning genomes with MUMmer intermediate New | Use MUMmer to align two bacterial genomes and visualize the results with Circa. | |
| Viral Amplicon Sequencing intermediate | Analyze viral amplicon sequence data using a real SARS-CoV-2 dataset. | |
| Viral Phylogenetics intermediate New | Perform viral phylogenetics analysis using real SARS-COV2 whole-genome sequences. | |
| Efficient sequence analysis with bqtools beginner New | Exploring bqtools, a toolkit for working with and manipulating BINSEQ files | |
| Variant calling advanced | Use variant calling to decode a secret message stored in sequencing data. | |
| Building trees with SKA intermediate | Use ska.rust to compare and align closely related small genomes using split k-mers |
| Terminal Basics beginner | Get up to speed with the terminal. Start here if you're new to bioinformatics. | |
| JSON wrangling with jq beginner | Filter and wrangle JSON files on the command-line using jq. | |
| Data exploration with awk intermediate | Filter, extract and transform tabular data (TSV files) using awk. | |
| How to write a Bash script beginner New | How to turn your one-liners into reusable command-line scripts | |
| Terminal Exercises intermediate New | Command-line exercises from the Carpentries' Unix Shell lesson. |