808 Open source projects that are alternatives of or similar to Pygeno

cython + htslib == fast VCF and BCF processing

annotate a VCF with other VCFs/BEDs/tabixed files

Bayesian genotyper for structural variants

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

Scalable genomic data analysis.

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

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

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.

Official code repository for GATK versions 4 and up

A modern genome browser built with JavaScript and HTML5.

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

A genome browser that shows long reads and complex variants better

A collection of scripts and notes related to genomics and bioinformatics

Haplotype VCF comparison tools

Java utilities for Bioinformatics

Scripts to download genomes from the NCBI FTP servers

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

A package for designing compact and comprehensive capture probe sets.

An open-access bioinformatics text

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

Ten Quick Tips for Deep Learning in Biology

Efficient variant-call data storage and retrieval library using the TileDB storage library.

GenomeTools genome analysis system.

A powerful open source data warehouse system

JavaScript VisualizationTools

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

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

Official git repository for Biopython (originally converted from CVS)

A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)

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

simple viewer for variant call format using htslib

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

De novo assembly based variant calling pipeline for Illumina short reads

Spark VCF data source implementation for Dataframes

An ultrafast memory-efficient short read aligner

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

Research on polio / protein folding.

A simple command-line tool to download data from Joint Genome Institute databases

Cancer Predisposition Sequencing Reporter (CPSR)

A faster lmm for GWAS. Supports GPU backend.

Example client programs for Saphetor's VarSome annotation API

Genomics using open source tools, running on GCP or AWS

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment

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

🔬 Assemble large genomes using short reads

Predict AMPs in (meta)genomes and peptides

Toolkit for preparing genomes for submission to NCBI

PERF is an Exhaustive Repeat Finder

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

Compute N50/NG50 and auN/auNG

Earl Grey: A fully automated TE curation and annotation pipeline

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

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

Method to optimally select samples for validation and resequencing

Feature Annotation Location Description Ontology

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

Assembling the cause of phenotypes and genotypes from NGS data

Fast hash function for DNA sequences

Bystro genetic analysis (annotation, filtering, statistics)

Provide R access to the NCI Genomic Data Commons portal.