Interactive bioinformatics tutorials

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Screenshot of terminal and exercises

Tutorials

Data exploration
beginner terminal
Terminal Basics

Get up to speed with the terminal. Start here if you're new to bioinformatics.

beginner terminal exercises carpentries new
Terminal Exercises

Command-line exercises from the Carpentries' Unix Shell lesson.

beginner jq terminal
JSON wrangling with jq

Filter and wrangle JSON files on the command-line using jq.

intermediate awk terminal
Data exploration with awk

Filter, extract and transform tabular data (TSV files) using awk.

File formats
beginner bedtools igv
Genomic intervals with bedtools

Explore and wrangle .bed files with bedtools.

beginner samtools IGV
BAM parsing with samtools

Explore and wrangle .sam/.bam files with samtools.

Quality control
beginner fastp QC sequencing
DNA sequencing QC

Evaluate the quality of a sequencing run by running fastp on your FASTQ files.

beginner igv
Visualize variants with IGV

Distinguish real variants from artifacts using the IGV genome browser.

Data analysis
beginner bowtie2 bcftools
Sequence alignment with bowtie2

Align reads to a reference genome.

beginner blastn blastp new
Sequence alignment with BLAST

Use BLAST to align DNA and protein sequences.

beginner kmer counting jellyfish new
K-mer counting with Jellyfish

Learn the basics of k-mer counting using Jellyfish

intermediate bowtie2 bcftools
Variant calling

Use variant calling to decode a secret message stored in sequencing data.

intermediate ViralConsensus minimap
Viral Amplicon Sequencing

Analyze viral amplicon sequence data using a real SARS-CoV-2 dataset.

difficult samtools bedtools grep
Debugging Puzzles

Debug file format issues that are commonly seen in genomics.

Playgrounds

command line terminal bash

Command Line

Command line for open-ended exploration

awk

Awk

Filter and wrangle tabular data

jq json

Jq

Filter and wrangle JSON data

grep regex

Grep

Search and filter utility

sed regex

Sed

Search and replace utility

Explore

smith-waterman needleman-wunsch

Align DNA sequences

Explore the Smith-Waterman and Needleman-Wunsch sequence alignment algorithms.

wgsim

Simulate DNA sequences

Simulate DNA sequencing reads with wgsim.

t-SNE

t-SNE algorithm

Run t-SNE on single-cell sequencing data.

fastp

QC reports for FASTQ files

Generate data quality reports with fastp.