1011 Open source projects that are alternatives of or similar to bacnet

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

A fast 23andMe genome text file parser, now superseded by arv

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

Rapid large-scale prokaryote pan genome analysis

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

A genome browser that shows long reads and complex variants better

Earl Grey: A fully automated TE curation and annotation pipeline

Official git repository for Biopython (originally converted from CVS)

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

Compute N50/NG50 and auN/auNG

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

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

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

Deep learning infrastructure for bioinformatics

Reads simulator

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

An ultrafast memory-efficient short read aligner

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

A powerful open source data warehouse system

dysgu-SV is a collection of tools for calling structural variants using short or long reads

Open source Java library for computational proteomics

A package for designing compact and comprehensive capture probe sets.

Fast hash function for DNA sequences

Assembling the cause of phenotypes and genotypes from NGS data

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

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

An ontology of cell types

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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

Bayesian haplotype-based mutation calling

Predict plasmids from uncorrected long read data

Ten Quick Tips for Deep Learning in Biology

GenomeTools genome analysis system.

nim wrapper for htslib for parsing genomics data files

🔬 BEDOPS: high-performance genomic feature operations

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

cython + htslib == fast VCF and BCF processing

Intuitive local web frontend for the BLAST bioinformatics tool

Haplotype VCF comparison tools

JavaScript VisualizationTools

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

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

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

Toolkit for preparing genomes for submission to NCBI

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

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

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

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

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

A faster lmm for GWAS. Supports GPU backend.

Provide R access to the NCI Genomic Data Commons portal.

An open-access bioinformatics text

Fast alignment and preprocessing of chromatin profiles

Feature Annotation Location Description Ontology

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

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

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

Bystro genetic analysis (annotation, filtering, statistics)

A curated list of awesome bioinformatics software.

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics