682 Open source projects that are alternatives of or similar to Scaff10X

A genome browser that shows long reads and complex variants better

GenomeTools genome analysis system.

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

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

Official code repository for GATK versions 4 and up

A package for designing compact and comprehensive capture probe sets.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

A fast whole-genome aligner based on de Bruijn graphs

GCP Essentials for Bioinformatics Researchers

Inference of ploidy and heterozygosity structure using whole genome sequencing data

🌈Scaffold genome sequence assemblies using linked read sequencing data

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

Bioinformatics library for .NET

Bayesian genotyper for structural variants

A tool to circularize genome assemblies

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

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

Bayesian haplotype-based mutation calling

A collection of scripts and notes related to genomics and bioinformatics

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

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A faster lmm for GWAS. Supports GPU backend.

Reads simulator

Ten Quick Tips for Deep Learning in Biology

Deep learning infrastructure for bioinformatics

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

Model and predict short DNA sequence features with neural networks

An interactive web tool for quality control of DNA sequencing data

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

Genomics Extension for SQLite

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

Antimicrobial Resistance Identification By Assembly

Analysis pipelines for sequencing data

NGLess: NGS with less work

A cool place to store your Hi-C

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

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

nim wrapper for htslib for parsing genomics data files

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 powerful open source data warehouse system

Rapid large-scale prokaryote pan genome analysis

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

Next generation sequencing reads de novo assembler.

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

Intuitive local web frontend for the BLAST bioinformatics tool

🔬 BEDOPS: high-performance genomic feature operations

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

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

An ultrafast memory-efficient short read aligner

cython + htslib == fast VCF and BCF processing

Official git repository for Biopython (originally converted from CVS)

Haplotype VCF comparison tools

🔬 Assemble large genomes using short reads

JavaScript VisualizationTools

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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