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

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

Find causal cell-types underlying complex trait genetics

Tools to process and analyze deep sequencing data.

An ontology of cell types

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

A curated list of awesome bioinformatics software.

Python library to handle Gene Ontology (GO) terms

Fast alignment and preprocessing of chromatin profiles

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

Assembling the cause of phenotypes and genotypes from NGS data

The next version of bwa-mem

An open-access bioinformatics text

Bayesian genotyper for structural variants

Feature Annotation Location Description Ontology

A modern genome browser built with JavaScript and HTML5.

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

RADseq Data Exploration, Manipulation and Visualization using R

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

Ultra-fast and memory-efficient (meta-)genome assembler

Compute N50/NG50 and auN/auNG

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

A package for designing compact and comprehensive capture probe sets.

Efficient pythonic random access to fasta subsequences

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

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

echt rapid variant annotation and filtering

An open source platform for managing and analyzing biomedical big data

Data Wrangling and Processing for Genomics

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

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

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

PERF is an Exhaustive Repeat Finder

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

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

annotate a VCF with other VCFs/BEDs/tabixed files

Toolkit for preparing genomes for submission to NCBI

Development repository for the Bioconductor package 'mixOmics '

A faster lmm for GWAS. Supports GPU backend.

Fast genome-wide functional annotation through orthology assignment

My collection of light bioinformatics analysis pipelines for specific tasks

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

A modular annotation tool for genomic variants

Example client programs for Saphetor's VarSome annotation API

pythonic wrapper for htslib

An interactive web tool for quality control of DNA sequencing data

Clustering scRNAseq by genotypes

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

A Suite of Packages for Analysis of Big Genomic Data

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

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.

Learn interpretable computational phenotyping models from k-merized genomic data

Framework for building fast genomics web tools with WebAssembly and WebWorkers

BACNET is a Java based platform to develop website for multi-omics analysis

Script to automatically create and run IGV snapshot batchscripts

Pan-genome wide association studies

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

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

Scalable genomic data analysis.

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.