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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.

Universal chart comprehension and reasoning model

The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research).

Circlator is a tool to circularize genome assemblies. It will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly.

The AOPO provides classes and relationships for the semantic representation of the Adverse Outcome Pathway framework.

k-mer counting, filtering, and graph traversal.

NOVOPlasty - The organelle assembler and heteroplasmy caller. NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes..

A VCF Parser for Python.

Displaying sequence statistics for next-generation sequencing.

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.

Open source web framework for small molecule analysis based on Django.

Learning nonlinear operators

AI for chemical reaction prediction and synthesis planning

FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities.

This proposed vocabulary allows edges in Property Graphs (e.g Neo4j, RDF*) to be augmented with edge properties that specify ontological semantics, including (but not limited) to OWL-DL interpretations. [from GitHub]

Finds SNP sites from a multi-FASTA alignment file.

The Reagent Ontology (ReO) adheres to OBO Foundry principles (obofoundry.org) to model the domain of biomedical research reagents, considered broadly to include materials applied “chemically” in scientific techniques to facilitate generation of data and research materials. ReO is a modular ontology that re-uses existing ontologies to facilitate cross-domain interoperability. It consists of reagents and their properties, linking diverse biological and experimental entities to which they are related. ReO supports community use cases by providing a flexible, extensible, and deeply integrated framework that can be adapted and extended with more specific modeling to meet application needs.

Customizable pipeline for differential expression analysis with an intuitive GUI.

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

Horizon chart D3-based JavaScript library for DNA data.