398 Open source projects that are alternatives of or similar to Kaiju

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

A DSL for data-driven computational pipelines

Application for making ENCODE Blacklists

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Inference of ploidy and heterozygosity structure using whole genome sequencing data

nim wrapper for htslib for parsing genomics data files

Bioinformatics library for .NET

APBS - software for biomolecular electrostatics and solvation

Benchmarking programming languages/implementations for common tasks in Bioinformatics

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

A Practical and Efficient NCBI Taxonomy Toolkit

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

A collection of scripts and notes related to genomics and bioinformatics

Single cell perturbation prediction

Antimicrobial Resistance Identification By Assembly

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

FastQC port to Qt5: A quality control tool for high throughput sequence data.

dna2vec: Consistent vector representations of variable-length k-mers

A robust and fast clustering method for amplicon-based studies

Simple simulation of single-cell RNA sequencing data

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

An efficient FASTQ manipulation suite

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Bioinformatics Workbook repository

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

Python module for average nucleotide identity analyses

Bayesian haplotype-based mutation calling

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

ECG classification programs based on ML/DL methods

SortMeRNA: next-generation sequence filtering and alignment tool

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Code examples of fast and simple k-mer counters for tutorial purposes

pymzML - an interface between Python and mzML Mass spectrometry Files

A comprehensive library for computational molecular biology

Demonstrating best practices for bioinformatics command line tools

A tool to circularize genome assemblies

✏️ A versatile DNA sequence optimizer

A curated list of bioinformatics bench-marking papers and resources.

GCP Essentials for Bioinformatics Researchers

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

Race and ethnicity Imputation from Disease history with Deep LEarning

Fast multi-line FASTA/Q reader in several programming languages

Genomics Extension for SQLite

NGLess: NGS with less work

MOLGENIS - for scientific data: management, exploration, integration and analysis.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A curated list of awesome Bioinformatics libraries and software.

A cool place to store your Hi-C

Post-analysis of immune repertoire sequencing data

Bio4j abstract model and general entry point to the project

Package for fetching metadata and downloading data from SRA/ENA/GEO

parallel fastq-dump wrapper

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

UGENE is free open-source cross-platform bioinformatics software