619 Open source projects that are alternatives of or similar to netSmooth

An open-access bioinformatics text

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

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Bystro genetic analysis (annotation, filtering, statistics)

Bayesian haplotype-based mutation calling

Assembling the cause of phenotypes and genotypes from NGS data

Ten Quick Tips for Deep Learning in Biology

Provide R access to the NCI Genomic Data Commons portal.

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

A tool to circularize genome assemblies

Fast hash function for DNA sequences

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

nim wrapper for htslib for parsing genomics data files

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

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

Rapid large-scale prokaryote pan genome analysis

GenomeTools genome analysis system.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

An ultrafast memory-efficient short read aligner

cython + htslib == fast VCF and BCF processing

Bead-based single-cell atac processing

JavaScript VisualizationTools

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

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

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

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

NGLess: NGS with less work

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

A cool place to store your Hi-C

Compute N50/NG50 and auN/auNG

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

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

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

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

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

Reads simulator

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

A genome browser that shows long reads and complex variants better

Deep learning infrastructure for bioinformatics

A powerful open source data warehouse system

A collection of scripts and notes related to genomics and bioinformatics

A package for designing compact and comprehensive capture probe sets.

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

Official git repository for Biopython (originally converted from CVS)

🔬 BEDOPS: high-performance genomic feature operations

CUT&RUN and CUT&Tag data processing and analysis

Haplotype VCF comparison tools

mgatk: mitochondrial genome analysis toolkit

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

Toolkit for preparing genomes for submission to NCBI

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

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

A faster lmm for GWAS. Supports GPU backend.

Antimicrobial Resistance Identification By Assembly

Inference of ploidy and heterozygosity structure using whole genome sequencing data

Intuitive local web frontend for the BLAST bioinformatics tool

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

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

Fast alignment and preprocessing of chromatin profiles