1142 Open source projects that are alternatives of or similar to Hail

highly-efficient & lightweight mutation signature matrix aggregation

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

Model and predict short DNA sequence features with neural networks

An interactive web tool for quality control of DNA sequencing data

Data intensive science for everyone.

The next version of bwa-mem

Structural variant toolkit for VCFs

Bioinformatics library for .NET

List of tools and resources related to the 10x Genomics GEMCode/Chromium system

Antimicrobial Resistance Identification By Assembly

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.

A Java API for high-throughput sequencing data (HTS) formats.

Earl Grey: A fully automated TE curation and annotation pipeline

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

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

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Code examples of fast and simple k-mer counters for tutorial purposes

Syntax highlighting for computational biology

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

A fast and sensitive gapped read aligner

A tool to circularize genome assemblies

A genome browser that shows long reads and complex variants better

Deep learning infrastructure for bioinformatics

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

Toolset for SV simulation, comparison and filtering

🔬 BEDOPS: high-performance genomic feature operations

Proof-of-concept seq-to-graph mapper and graph generator

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

An open-source toolkit for large-scale genomic analysis

simple viewer for variant call format using htslib

A React web application to query and share any PostgreSQL database.

A high-performance, Pythonic language for bioinformatics

A faster lmm for GWAS. Supports GPU backend.

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

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

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

Fast hash function for DNA sequences

Compute N50/NG50 and auN/auNG

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

Bystro genetic analysis (annotation, filtering, statistics)

Method to optimally select samples for validation and resequencing

Provide R access to the NCI Genomic Data Commons portal.

JavaScript VisualizationTools

Genotyping of segregating mobile elements insertions

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

Predict plasmids from uncorrected long read data

Fast alignment and preprocessing of chromatin profiles

De novo assembly based variant calling pipeline for Illumina short reads

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

Example client programs for Saphetor's VarSome annotation API

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

Official git repository for Biopython (originally converted from CVS)

Assembling the cause of phenotypes and genotypes from NGS data

A comprehensive tutorial about GWAS and PRS

An open source platform for managing and analyzing biomedical big data

Efficient pythonic random access to fasta subsequences

Code for Agile Data Science 2.0, O'Reilly 2017, Second Edition

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