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

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

GA4GH Variation Representation Python Implementation

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

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

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

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

A method for variant graph genotyping based on exact alignment of k-mers

Development repository for the Bioconductor package 'mixOmics '

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

echt rapid variant annotation and filtering

Deep learning infrastructure for bioinformatics

Antimicrobial Resistance Identification By Assembly

A secure encryption tool for genomic data

Mandrake 🌿/👨‍🔬🦆 – Fast visualisation of the population structure of pathogens using Stochastic Cluster Embedding

(No maintenance) Detect gene fusion directly from raw fastq files

Data Wrangling and Processing for Genomics

Estimation of pairwise distances under a probabilistic framework

Framework for building fast genomics web tools with WebAssembly and WebWorkers

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

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

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

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

Project metadata manager for PEPs in Python

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

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

Method to optimally select samples for validation and resequencing

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

Scalable long read self-correction and assembly polishing with multiple sequence alignment

Fast large scale matrix visualization for the web.

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Toolkit for preparing genomes for submission to NCBI

use the noise

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

A faster lmm for GWAS. Supports GPU backend.

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

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

My collection of light bioinformatics analysis pipelines for specific tasks

Utilities for analyzing next generation sequencing data.

RADseq Data Exploration, Manipulation and Visualization using R

myVCF: a web-based platform for target and exome mutations data management

A modular annotation tool for genomic variants

JavaScript VisualizationTools

The GenePattern Server web application

AQUAS TF and histone ChIP-seq pipeline

De novo assembly based variant calling pipeline for Illumina short reads

DriverPower

pythonic wrapper for htslib

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

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

RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.

Clustering scRNAseq by genotypes

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

Bayesian haplotype-based mutation calling

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

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

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

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Seven Bridges Genomics aligner/caller debugging and analysis tools

A WGS de novo assembler based on the FMD-index for large genomes

Ten Quick Tips for Deep Learning in Biology