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

Scripts to download genomes from the NCBI FTP servers

A Kotlin DSL and library to create and plot RNA 2D structures

SortMeRNA: next-generation sequence filtering and alignment tool

Open source Java library for computational proteomics

BWK awk modified for biological data

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Command line tool to run batch jobs concurrently with ETL framework on AWS or other cloud computing resources

Tools to process and analyze deep sequencing data.

Improving genome bins through the combination of different binning programs

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

📊 Codon usage tables in code-friendly format + Python bindings

MMseqs2: ultra fast and sensitive search and clustering suite

Classify sequencing reads using MinHash.

compacted de Bruijn graph construction in low memory

Single Cell Analysis Pipelines

d3 library to build circular graphs

A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.

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

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

Bioinformatics containers

A permissively licensed library designed to replace Illumina's Experiment Manager

🌈Scaffold genome sequence assemblies using linked read sequencing data

Genomics using open source tools, running on GCP or AWS

Tools for working with SAM/BAM data

R mased batch sequence downloader, with primer development and in silico evaluation capabilities

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

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Python library to facilitate genome assembly, annotation, and comparative genomics

Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads

Genome inference from a population reference graph

A faster lmm for GWAS. Supports GPU backend.

A fast and sensitive gapped read aligner

Structural variation caller using third generation sequencing

pymzML - an interface between Python and mzML Mass spectrometry Files

Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.

Plant image analysis using OpenCV

JavaScript VisualizationTools

LAMBDA – the Local Aligner for Massive Biological DatA

Core BioPerl 1.x code

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

Strelka2 germline and somatic small variant caller

A comprehensive library for computational molecular biology

Quickly search, compare, and analyze genomic and metagenomic data sets.

A scikit-learn compatible library for graph kernels

Examples of using deep learning in Bioinformatics

Model and predict short DNA sequence features with neural networks

Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.

Open-source bioinformatics components for Dash

🔬 Assemble large genomes using short reads

Demonstrating best practices for bioinformatics command line tools

Interactive network visualization in Python and Dash, powered by Cytoscape.js

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

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Efficient variant-call data storage and retrieval library using the TileDB storage library.

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways