1911 Open source projects that are alternatives of or similar to Bedops

A collection of useful utility functions

GenomeTools genome analysis system.

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

A cross-platform command-line tool for executing jobs in parallel

Analysis pipelines for sequencing data

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Data intensive science for everyone.

Proof-of-concept seq-to-graph mapper and graph generator

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Model and predict short DNA sequence features with neural networks

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

A powerful open source data warehouse system

A collection of publications on comparison of high-throughput sequencing technologies.

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

A fast whole-genome aligner based on de Bruijn graphs

Bayesian genotyper for structural variants

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

A DSL for data-driven computational pipelines

Genomics Extension for SQLite

Antimicrobial Resistance Identification By Assembly

A collection of scripts and notes related to genomics and bioinformatics

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

A tool to circularize genome assemblies

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

A genome browser that shows long reads and complex variants better

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Bayesian haplotype-based mutation calling

nim wrapper for htslib for parsing genomics data files

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Official code repository for GATK versions 4 and up

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

DEPRECIATED! Please use nf-core/tools instead

An interactive web tool for quality control of DNA sequencing data

Robust and efficient workflows using a simple language agnostic approach

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

Flexible genotype query among 30,000+ samples whole-genome

GCP Essentials for Bioinformatics Researchers

Bioinformatics library for .NET

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Robust, flexible and resource-efficient pipelines using Go and the commandline

NGLess: NGS with less work

A cool place to store your Hi-C

UGENE is free open-source cross-platform bioinformatics software

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

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

A repository for setting up a RNAseq workflow

c++ LINQ -like library of higher-order functions for data manipulation

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

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

Deep learning infrastructure for bioinformatics

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

Intuitive local web frontend for the BLAST bioinformatics tool

Scalable genomic data analysis.

Reads simulator

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

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