273 Open source projects that are alternatives of or similar to Smoove

Model and predict short DNA sequence features with neural networks

Official code repository for GATK versions 4 and up

Antimicrobial Resistance Identification By Assembly

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

variant expressions, annotation, and filtering for great good.

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

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

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Genomics Extension for SQLite

A fast whole-genome aligner based on de Bruijn graphs

Scalable genomic data analysis.

A cool place to store your Hi-C

A friendly next-generation interface for Genomic data discovery powered by InterMine

Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls

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

A collection of scripts and notes related to genomics and bioinformatics

Analysis pipelines for sequencing data

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A list of web-based interactive biological data visualizations.

GCP Essentials for Bioinformatics Researchers

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

A tool to circularize genome assemblies

Data intensive science for everyone.

Script to automatically create and run IGV snapshot batchscripts

Bayesian genotyper for structural variants

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

An R package for creating Q-Q and manhattan plots from GWAS results

An interactive web tool for quality control of DNA sequencing data

MISO: An open-source LIMS for NGS sequencing centres

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

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

A collaboratively written review paper on deep learning, genomics, and precision medicine

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

Development repository for the Bioconductor package 'mixOmics '

Simulate genealogical trees and genomic sequence data using population genetic models

Framework for building fast genomics web tools with WebAssembly and WebWorkers

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

Guided synteny alignment between duplicated genomes (within specified quota constraint)

Inference of ploidy and heterozygosity structure using whole genome sequencing data

igv.js server and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"

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

RADseq Data Exploration, Manipulation and Visualization using R

AQUAS TF and histone ChIP-seq pipeline

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

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

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

Bioinformatics library for .NET

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

Bayesian haplotype-based mutation calling

A Suite of Packages for Analysis of Big Genomic Data

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

tools for working with genome variation graphs

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

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

Genomic Data Retrieval with R

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

nim wrapper for htslib for parsing genomics data files

NGLess: NGS with less work

Pan-genome wide association studies