395 Open source projects that are alternatives of or similar to MGSE

A package for designing compact and comprehensive capture probe sets.

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

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

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

A fast tool for hybrid genome assembly of long and short reads

No description or website provided.

Official code repository for GATK versions 4 and up

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

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

Genomic Data Retrieval with R

Close assembly gaps using long-reads at high accuracy.

Command line utility for manipulating Illumina-generated FastQ files.

🐳 Bio-dockers: dockerized bioinformatic tools

A library for manipulating bioinformatics sequencing formats in Apache Spark

Collection of scripts for bacterial genomics

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.

Reference-based transcript discovery from long RNA read

Large genome reassembly based on Hi-C data, continuation of GRAAL

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

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

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

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.

NGLess: NGS with less work

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

GenomeTools genome analysis system.

De novo genome assembly and multisample variant calling

PERF is an Exhaustive Repeat Finder

Nanopore sequence read simulator

Viral genomics analysis pipelines

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

A genome browser that shows long reads and complex variants better

Java utilities for Bioinformatics

Data intensive science for everyone.

An accurate and ultra-fast hybrid genome assembler

Tools to process and analyze deep sequencing data.

Ultrafast sequence typing and gene detection from NGS raw reads

Predict plasmids from uncorrected long read data

🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

A Java API for high-throughput sequencing data (HTS) formats.

Reads simulator

Performant Pythonic GenomicRanges

Rapid large-scale prokaryote pan genome analysis

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

A DNA Sequence Alignment/Map (SAM) library for Clojure

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

An open-source toolkit for large-scale genomic analysis

🔬 BEDOPS: high-performance genomic feature operations

Tools to work with variant call format files

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

Haplotype VCF comparison tools

SDK for GPU accelerated genome assembly and analysis

structural variant calling and genotyping with existing tools, but, smoothly.

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

Fast large scale matrix visualization for the web.

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

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

JavaScript VisualizationTools

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦