339 Open source projects that are alternatives of or similar to Clair3

PEPPER-Margin-DeepVariant

Predict plasmids from uncorrected long read data

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

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

Collection of scripts for bacterial genomics

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

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Ultrafast sequence typing and gene detection from NGS raw reads

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

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

De novo genome assembly and multisample variant calling

De novo assembly based variant calling pipeline for Illumina short reads

Clustering scRNAseq by genotypes

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

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

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

Complex structural variant detection from WGS data

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

A tool for fast and accurate summarizing of variant calling format (VCF) files

simple viewer for variant call format using htslib

GA4GH Variation Representation Python Implementation

A secure encryption tool for genomic data

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

Improve the quality of a denovo assembly by scaffolding and gap filling

Manhattan plot Generator

use the noise

Fast and accurate gene fusion detection from RNA-Seq data

📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology

Contact map analysis for biomolecules; based on MDTraj

A curated list of awesome computational cryo-EM methods.

Analysing Capture Seq Count Data

The GenePattern Server web application

Examples to get started with IBM Functional Genomics Platform

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

Python-based UCSC genome browser snapshot-taker and gallery-maker

SneakySnake🐍 is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs…

💾 📃 "Reads to report" for public health and clinical microbiology

Spatial alignment of single cell transcriptomic data.

Forward-time simulation in Python using fwdpp

DriverPower

CUT&RUN and CUT&Tag data processing and analysis

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

Population-wide Deletion Calling

SARS-CoV-2 workflow for nanopore sequence data

Big Compute Learning Labs

Explore rearrangements and copy-number amplifications in a cancer genome

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

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

Introduction to the Command Line for Genomics

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data

phenol: Phenotype ontology library

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

TideHunter: efficient and sensitive tandem repeat detection from noisy long reads using seed-and-chain

a pileup library that embraces the huge

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

A Curated List of Computational Biology Datasets Suitable for Machine Learning

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Bead-based single-cell atac processing