322 Open source projects that are alternatives of or similar to mccortex

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

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

Complex structural variant detection from WGS data

Predict plasmids from uncorrected long read data

Earl Grey: A fully automated TE curation and annotation pipeline

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

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

De novo assembly based variant calling pipeline for Illumina short reads

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

LRSDAY: Long-read Sequencing Data Analysis for Yeasts

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

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

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

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

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

Ultrafast sequence typing and gene detection from NGS raw reads

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

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

Version 2.1.0 released

A curated list of awesome bioinformatics software.

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

(WIP) best-practices workflow for rare disease

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

A package for designing compact and comprehensive capture probe sets.

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

Example with Cortex V2 API

Introduction to Cloud Computing for Genomics

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

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

echt rapid variant annotation and filtering

Compute N50/NG50 and auN/auNG

Sentieon DNAseq

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.

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

Fast alignment and preprocessing of chromatin profiles

Fast hash function for DNA sequences

GraphBin: Refined binning of metagenomic contigs using assembly graphs

Toolkit for k-mer with taxonomic information

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Data Wrangling and Processing for Genomics

A fast 23andMe genome text file parser, now superseded by arv

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

Assembling the cause of phenotypes and genotypes from NGS data

Simple pure Python SAM parser and objects for working with SAM records

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

Provide R access to the NCI Genomic Data Commons portal.

An interactive web portal for exploring immuno-oncology data

PERF is an Exhaustive Repeat Finder

Inference of switch-like differential expression along single-cell trajectories

VisualQC : assistive tool to ease the quality control workflow of neuroimaging data.

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

Classify sequencing reads using MinHash.

An open-access bioinformatics text

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

ARM® Cortex®-M platform crate for Drone, an Embedded Operating System.

Find causal cell-types underlying complex trait genetics

Genetic Map Comparison

Modular Multi-scale Integrated Genome Graph Browser

Genomics using open source tools, running on GCP or AWS