56 Open source projects that are alternatives of or similar to MUMandCo

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

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Identification of segmental duplications in the genome

Tools for processing and analyzing structural variants.

Graph based multi genome aligner

An efficient index for the colored, compacted, de Bruijn graph

Workflow for Building Microsynteny Networks

SuperPhy for the semantic web

Research on polio / protein folding.

Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA

dcHiC: Differential compartment analysis for Hi-C datasets

Das Robert Koch-Institut stellt Systeme zur bundesweiten molekularen Surveillance des SRARS-CoV-2-Virus bereit. Jedes Labor in Deutschland, das SARS-CoV-2 sequenziert, ist laut der Verordnung zur molekulargenetischen Surveillance des Coronavirus SARS-CoV-2 verpflichtet, dem Robert Koch-Institut die Sequenz- und zugehörige Metadaten zu übermittel…

The Modular Aligner and The Modular SV Caller

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

Nanopore sequence read simulator

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

A fast 23andMe DNA parser and inferrer for Python

Fast and accurate gene fusion detection from RNA-Seq data

Genome Interval Arithmetic in R

Understand DNA structure and how machine learning can be used to work with DNA sequence data.

Population-wide Deletion Calling

De novo annotation of young retrotransposons

simuG: a general-purpose genome simulator

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

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

🔬 Assemble large genomes using short reads

Download and use genomes the easy way.

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

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

GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

Viral genomics analysis pipelines

Next generation sequencing reads de novo assembler.

Genomic Data Retrieval with R

Genome annotation with AUGUSTUS

🌈Scaffold genome sequence assemblies using linked read sequencing data

Official code repository for GATK versions 4 and up

Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

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

🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus

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.

parallelized blat with multi-threads support

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

A package for designing compact and comprehensive capture probe sets.

PERF is an Exhaustive Repeat Finder

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.

Allele-specific copy number estimation with whole genome sequencing

Method to optimally select samples for validation and resequencing

Complex structural variant detection from WGS data

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