GPT4All: Run Local LLMs on Any Device. Open-source and available for commercial use.

Explorer++ is a lightweight and fast file manager for Windows

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

SPAdes Genome Assembler

The second version of the Kraken taxonomic sequence classification system

Ultra-fast and memory-efficient (meta-)genome assembler

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Mummer alignment tool

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Transcript assembly and quantification for RNA-Seq

Fast Whole-Genome Similarity (ANI) Estimation

Fast genome and metagenome distance estimation using MinHash

CryptSync is a small utility that synchronizes two folders while encrypting the contents in one folder. That means one of the two folders has all files unencrypted (the files you work with) and the…

Genome browser and variant annotation

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

🔬 Assemble large genomes using short reads

Genome annotation with AUGUSTUS

Bayesian haplotype-based mutation calling

SortMeRNA: next-generation sequence filtering and alignment tool

Program for analysing NGS data.

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads

A gap-closing software tool that uses long reads to enhance genome assembly.

A tool for estimating repeat sizes

Population-scale genotyping using pangenome graphs

DRAGEN open-source mapper

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

Short-read and long-read sequencing tools for diagnostics

Version 5 of the CAFE phylogenetics software

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output inc…

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.