595 Open source projects that are alternatives of or similar to dysgu

Strelka2 germline and somatic small variant caller

A Python library to visualize and analyze long-read transcriptomes

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

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Tools for analyzing 10X Genomics data

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Quickly search, compare, and analyze genomic and metagenomic data sets.

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

Explore rearrangements and copy-number amplifications in a cancer genome

Randomly subsample sequencing reads to a specified coverage

Examples of using deep learning in Bioinformatics

A permissively licensed library designed to replace Illumina's Experiment Manager

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

Minor Variant Calling and Phasing Tools

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

A comprehensive library for computational molecular biology

A full spaCy pipeline and models for scientific/biomedical documents.

🔬 Assemble large genomes using short reads

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.

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

React component for Cytoscape.js network visualisations

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

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

use the noise

Fast multi-line FASTA/Q reader in several programming languages

A curated list of resources for learning bioinformatics.

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

Environmental DNA metabarcoding taxonomic identification

JAMP - Just Another Metabarcoding Pipeline

an implementation of NSGA-II in java

Ultrafast sequence typing and gene detection from NGS raw reads

Data and analysis for the Splatter paper

Simple simulation of single-cell RNA sequencing data

Resource of human chromosome schematics & images

The GenePattern Server web application

Python package for graph neural networks in chemistry and biology

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

BELLA: a Computationally-Efficient and Highly-Accurate Long-Read to Long-Read Aligner and Overlapper

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Salentin et al. (2015), https://www.doi.org/10.1093/nar/gkv315

A plotly.js React component from Plotly 📈

RAxML Next Generation: faster, easier-to-use and more flexible

DriverPower

ECG classification programs based on ML/DL methods

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

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

Analysing Capture Seq Count Data

Genomics using open source tools, running on GCP or AWS

The Ensembl Compara Perl API and SQL schema

Tools for processing and analyzing structural variants.

Multilocus sequence typing by blast using the schemes from PubMLST

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

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Biostar Q&A

A fast, scalable, and accurate local ancestry method.

Single cell perturbation prediction

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

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

Application for making ENCODE Blacklists

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