438 Open source projects that are alternatives of or similar to Sambamba

A D library for computational biology and bioinformatics

C library for high-throughput sequencing data formats

Simple pure Python SAM parser and objects for working with SAM records

Example client programs for Saphetor's VarSome annotation API

👁 Python library to plot DNA sequence features (e.g. from Genbank files)

A comprehensive tutorial about GWAS and PRS

A scikit-learn compatible library for graph kernels

Aim to be the bioinformatics repository with more and newer packages

The Chemistry Development Kit

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

WebLogo 3: Sequence Logos redrawn

A React web application to query and share any PostgreSQL database.

Bioinformatics one liners from Ming Tang

A lightweight middleware framework for functions as a service

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

Real-time species-typing visualisation for nanopore data.

Modular and universal bioinformatics

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

Signal-level algorithms for MinION data

Sample search by metadata and features

Accurate sample inference from amplicon data with single nucleotide resolution

Working with molecular structures in pandas DataFrames

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

An open source platform for managing and analyzing biomedical big data

Fast and accurate sequence demultiplexing

DOM Text Based Multiple Sequence Alignment Library

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

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

annotate a VCF with other VCFs/BEDs/tabixed files

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Efficient pythonic random access to fasta subsequences

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

A fast and sensitive gapped read aligner

Highly adaptable common interface for proteomics search and de novo engines

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

Cutadapt removes adapter sequences from sequencing reads

This library tackles the construction and efficient execution of computational chemistry workflows

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

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

The uncompromising Snakemake code formatter

A graphical text editor

Structural variant and indel caller for mapped sequencing data

MMseqs2 app to run on your workstation or servers

SAM: Sharpness-Aware Minimization (PyTorch)

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

A simple/sample AngularV4-based web app that demonstrates different API authentication options using Amazon Cognito and API Gateway with an AWS Lambda and Amazon DynamoDB backend that stores user details in a complete end to end Serverless fashion.

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

Welcome to the Innovator Island serverless workshop! This repo contains all the instructions and code you need to complete the workshop. Questions? Contact @jbesw.

The Microbiome Interpretable Temporal Rule Engine

An analysis and visualization platform for 'omics data

A simplified pipeline for ctDNA sequencing data analysis

Open-source bioinformatics components for Dash

Phylogenetic trees in Julia

COBRApy is a package for constraint-based modeling of metabolic networks.

The next version of bwa-mem

A modern genome browser built with JavaScript and HTML5.

Plant image analysis using OpenCV