295 Open source projects that are alternatives of or similar to rare-disease-wf

Numerical Encoding for Human Genetic Variants

Spark VCF data source implementation for Dataframes

xHLA: Fast and accurate HLA typing from short read sequence data

simple viewer for variant call format using htslib

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

A faster lmm for GWAS. Supports GPU backend.

Tools for analyzing 10X Genomics data

Predict AMPs in (meta)genomes and peptides

An interactive web portal for exploring immuno-oncology data

A modular annotation tool for genomic variants

A tool to plot significant regions of GWAS

Learn interpretable computational phenotyping models from k-merized genomic data

Toolkit for preparing genomes for submission to NCBI

Grammar of Scalable Linked Interactive Nucleotide Graphics

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

Variant types in TypeScript

My collection of light bioinformatics analysis pipelines for specific tasks

find large indels (in the blind spot between GATK/freebayes and SV callers)

Fast hash function for DNA sequences

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

pythonic wrapper for htslib

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Lollipop-diagram to interactively visualize genetic mutations

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Clustering scRNAseq by genotypes

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

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

mgatk: mitochondrial genome analysis toolkit

Data Wrangling and Processing for Genomics

Interactive assembly and analysis of RAD-seq data sets

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

An R framework for phylostratigraphy

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

A package for designing activity-informed nucleic acid diagnostics for viruses.

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

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

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

Resource of human chromosome schematics & images

Chanjo provides a better way to analyze coverage data in clinical sequencing.

A fast, scalable, and accurate local ancestry method.

A package for designing compact and comprehensive capture probe sets.

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Environmental DNA metabarcoding taxonomic identification

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

PERF is an Exhaustive Repeat Finder

Command line utility for manipulating Illumina-generated FastQ files.

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

echt rapid variant annotation and filtering

pathoscore evaluates variant pathogenicity tools and scores.

A proof of concept of RNAseq pipeline

Multilocus sequence typing by blast using the schemes from PubMLST

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

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

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

🐳 Bio-dockers: dockerized bioinformatic tools

Simple tagged unions

Complex structural variant detection from WGS data