Find open-source science resources

SPAdes (St. Petersburg genome assembler) is an assembly toolkit containing various assembly pipelines and the de-facto standard for prokaryotic genome assemblies.

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data.

A Swiss Army knife for genome arithmetic.

Pythonic Access to the Ensembl database.

lumpy: a general probabilistic framework for structural variant discovery.

Expertly curated genomics papers to get up to speed on genomics, RNA-seq, statistics (used in genomics), software development, and more.

Resources on ChIP-seq data which include papers, methods, links to software, and analysis.

[@crazyhottommy](https://github.com/crazyhottommy)'s notes on various steps and considerations when doing RNA-seq analysis.

Educational resource on performing RNA-seq analysis in the cloud using Amazon AWS cloud services. Topics include preparing the data, preprocessing, differential expression, isoform discovery, data visualization, and interpretation.

A collection of research papers for AI-based protein design.

List of resources on alternative splicing including software, databases, and other tools.

Solid path for those of you who want to complete a Bioinformatics course on your own time, for free, with courses from the best universities in the World.

A circos representation of multiple GWAS results.

Perl package for circular plots, which are well suited for genomic rearrangements.

JavaScript library for drawing canvas-based gene diagrams.

JavaScript library that can be used to generate interactive and highly customizable web-based genome browsers.

Point and click, cross platform suite for analysing and visualizing next-generation sequencing datasets.

JavaScript genome browser that is highly customizable via plugins and track customizations.

D3 JavaScript based genome viewer. Constructs SVGs.

Java-based browser. Fast, efficient, scalable visualization tool for genomics data and annotations. Handles a large variety of formats.

Horizon chart D3-based JavaScript library for DNA data.

Flexible circular visualization of genome-associated data with BioPerl and SVG.

BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.

Embeddable genome viewer. Integration data from a wide variety of sources, and can load data directly from popular genomics file formats including bigWig, BAM, and VCF.

Easy-to-use DNA sequence visualization tool that turns FASTA files into browser-based visualizations.

A fuzzy Bruijn graph approach to long noisy reads assembly

A haplotype-resolved assembler for accurate Hifi reads.

De novo assembler for single molecule sequencing reads using repeat graphs.

A single molecule sequence assembler for genomes large and small.

Bakta is a tool for the rapid & standardized annotation of bacterial genomes & plasmids. It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.

Prokka: rapid prokaryotic genome annotation. Prokka is one of the most cited annotation command line tools for microbial genome annotations.

Minimap2 is an pairwise aligner for genomic and spliced nucleotide sequences. It can perform the assembly-to-assembly alignment, and works with gzip'd FASTQ, FASTA formats. It also finds overlaps between long-reads.

SKESA is a de-novo sequence read assembler for microbial genomes. It uses conservative heuristics and is designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.

Scalable toolkit for analyzing single-cell gene expression data, including preprocessing, visualization, clustering, and trajectory inference.

A VCF Parser for Python.

Python wrapper for [samtools](https://github.com/samtools/samtools).

Pythonic access to FASTA files.

Python wrapper for [bedtools](https://github.com/arq5x/bedtools).

Python library for blazing-fast genomic interval operations and genomic file formats I/O on Polars DataFrames

Cython + HTSlib == fast VCF parsing; even faster parsing than pyVCF.

A port of [pyVCF](https://github.com/jamescasbon/PyVCF) using Cython for speed.

Access to Biological Web Services from Python.

Pythonic access to the UCSC Genome database.

Genetic variant annotation and effect prediction toolbox.

Predicts whether an amino acid substitution affects protein function.

**Comes with samtools!** - Reads simulator.

Tools for adding mutations to existing `.bam` files, used for testing mutation callers.

GFF and GTF file manipulation and interconversion.

Suite of tools to handle gene annotations in any GTF/GFF format.

VCF manipulation and statistics (e.g. linkage disequilibrium, allele frequency, Fst).