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

🔬 Assemble large genomes using short reads

nim wrapper for htslib for parsing genomics data files

Deep learning infrastructure for bioinformatics

Simple simulation of single-cell RNA sequencing data

Strelka2 germline and somatic small variant caller

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

Toolset for SV simulation, comparison and filtering

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

React component for Cytoscape.js network visualisations

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Reads simulator

Single cell perturbation prediction

JavaScript VisualizationTools

Application for making ENCODE Blacklists

Rapid large-scale prokaryote pan genome analysis

dna2vec: Consistent vector representations of variable-length k-mers

A curated list of resources for learning bioinformatics.

APBS - software for biomolecular electrostatics and solvation

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

An efficient FASTQ manipulation suite

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

UGENE is free open-source cross-platform bioinformatics software

Annotated data.

Benchmarking programming languages/implementations for common tasks in Bioinformatics

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

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

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

A Practical and Efficient NCBI Taxonomy Toolkit

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

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

Syntax highlighting for computational biology

A collection of scripts and notes related to genomics and bioinformatics

Intuitive local web frontend for the BLAST bioinformatics tool

Inference of ploidy and heterozygosity structure using whole genome sequencing data

The sources of the openSNP website

Antimicrobial Resistance Identification By Assembly

Examples of using deep learning in Bioinformatics

A DSL for data-driven computational pipelines

Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

FastQC port to Qt5: A quality control tool for high throughput sequence data.

Python package for graph neural networks in chemistry and biology

Bioinformatics library for .NET

Next generation sequencing reads de novo assembler.

A robust and fast clustering method for amplicon-based studies

Core BioPerl 1.x code

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

R package for analyzing single-cell RNA-seq data

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

RAxML Next Generation: faster, easier-to-use and more flexible

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry

Package for fetching metadata and downloading data from SRA/ENA/GEO

Structural variant toolkit for VCFs

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

parallel fastq-dump wrapper

Haplotype VCF comparison tools

A curated list of Cheminformatics libraries and software.

cython + htslib == fast VCF and BCF processing

An ultrafast memory-efficient short read aligner

GenomeTools genome analysis system.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads