617 Open source projects that are alternatives of or similar to adapt

A package for designing compact and comprehensive capture probe sets.

Official code repository for GATK versions 4 and up

A collection of scripts and notes related to genomics and bioinformatics

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Data intensive science for everyone.

UGENE is free open-source cross-platform bioinformatics software

NGLess: NGS with less work

Analysing Capture Seq Count Data

Numerical Encoding for Human Genetic Variants

tools for working with genome variation graphs

Python and C++ code for reading and writing genomics data.

Efficient pythonic random access to fasta subsequences

Analysis pipelines for sequencing data

A curated list of awesome bioinformatics software.

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A Java API for high-throughput sequencing data (HTS) formats.

Official git repository for Biopython (originally converted from CVS)

A fast 23andMe genome text file parser, now superseded by arv

programs and scripts, mainly python, for analyses related to nucleic or protein sequences

Java utilities for Bioinformatics

Collection of scripts for bacterial genomics

Ultrafast sequence typing and gene detection from NGS raw reads

Materials related to events I might attend, and to talks I am giving

Keras for Science

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Cellular Automata Simulator

🐳 Bio-dockers: dockerized bioinformatic tools

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Diagnostics is an application displaying the diagnostic reports from applications on macOS.

find large indels (in the blind spot between GATK/freebayes and SV callers)

Data, metadata, and software tools for the COSORE database of continuous soil respiration measurements

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

A fast, scalable, and accurate local ancestry method.

Python Materials Discovery Framework

A flexible plotting and data analysis tool.

Identify phage regions in bacterial genomes for masking purposes

Command line utility for manipulating Illumina-generated FastQ files.

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Spark VCF data source implementation for Dataframes

ESP Insights: A remote diagnostics/observability framework for connected devices

Chemistry, Gamified

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

WebAssembly modules for genomics

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Hybrid memtest running in kernel mode, and userspace.

Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.

Fit models to your data in Python with Sherpa.

Predict AMPs in (meta)genomes and peptides

A tool to plot significant regions of GWAS

The most over-engineered and overpowered C++ assertion library.

Discrete Fourier transform

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Curated list of FREE emergency resources when you find yourself in the inevitable pickle with Windows. PRs welcome!

Transcripts annotation and GO enrichment Fisher tests

View biological networks via Cytoscape.js and sbgn-ml

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Multi-platform stacker for deep-sky astrophotography.

pyOBDII remake - better than ever!

OOMMFTools is a set of utilities designed to assist OOMMF postprocessing