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

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Toolkit for preparing genomes for submission to NCBI

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

A tool to circularize genome assemblies

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

Intuitive local web frontend for the BLAST bioinformatics tool

Provide R access to the NCI Genomic Data Commons portal.

Compute N50/NG50 and auN/auNG

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

Fast alignment and preprocessing of chromatin profiles

A curated list of awesome bioinformatics software.

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

De novo assembly based variant calling pipeline for Illumina short reads

BACNET is a Java based platform to develop website for multi-omics analysis

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

Earl Grey: A fully automated TE curation and annotation pipeline

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

annotate a VCF with other VCFs/BEDs/tabixed files

An open source platform for managing and analyzing biomedical big data

A fast 23andMe genome text file parser, now superseded by arv

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

Java utilities for Bioinformatics

A fast and sensitive gapped read aligner

Efficient pythonic random access to fasta subsequences

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

Tools to process and analyze deep sequencing data.

A faster lmm for GWAS. Supports GPU backend.

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

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

Scalable genomic data analysis.

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

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

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Robust and efficient workflows using a simple language agnostic approach

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

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

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

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

GCP Essentials for Bioinformatics Researchers

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

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

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

NGLess: NGS with less work

A collection of scripts and notes related to genomics and bioinformatics

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

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

nim wrapper for htslib for parsing genomics data files

Inference of ploidy and heterozygosity structure using whole genome sequencing data

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

A simple command-line tool to download data from Joint Genome Institute databases

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Antimicrobial Resistance Identification By Assembly

Bayesian haplotype-based mutation calling

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

Ten Quick Tips for Deep Learning in Biology