wtdbg2

A haplotype-resolved assembler for accurate Hifi reads.

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

JCVI is a versatile toolkit for comparative genomics analysis. It is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.

A Go library and command line utility for engineering organisms.

A single molecule sequence assembler for genomes large and small.

systemPipeR is a workflow management environment for reproducible data analysis that integrates R with command-line software. It enables researchers to design, execute, and report complex workflows on local machines and HPC systems. The framework combines R-based analysis with external tools through a Common Workflow Language (CWL) interface, manages workflow dependencies and restart capabilities, and automatically generates reproducible scientific analysis reports. The companion package systemPipeRdata provides ready-to-use workflow templates that simplify workflow setup and customization. Alternatively, workflow templates can be loaded from dedicated GitHub repositories.