440 Open source projects that are alternatives of or similar to spark-vcf

simple viewer for variant call format using htslib

Rare variant test software for next generation sequencing data

📊Evaluating, filtering, comparing, and visualising VCF

(WIP) best-practices workflow for rare disease

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Bayesian genotyper for structural variants

Learning the Variant Call Format

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

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

mgatk: mitochondrial genome analysis toolkit

annotate a VCF with other VCFs/BEDs/tabixed files

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

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

A phenotype-based tool for variant prioritization in WES and WGS data

A collection of scripts and notes related to genomics and bioinformatics

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

cython + htslib == fast VCF and BCF processing

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.

Haplotype VCF comparison tools

Powerful statistics for VCF files

Numerical Encoding for Human Genetic Variants

Home of the Genomic Feature and Variation Ontology (GFVO)

Scalable genomic data analysis.

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

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

Manhattan plot Generator

Analysing Capture Seq Count Data

CUT&RUN and CUT&Tag data processing and analysis

A library for manipulating bioinformatics sequencing formats in Apache Spark

convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations

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

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

Introduction to the Command Line for Genomics

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

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

Bioconductor package for management of multi-assay data

Forward-time simulation in Python using fwdpp

Multi-dimensional data arrays with labeled dimensions

Explore rearrangements and copy-number amplifications in a cancer genome

An encrypted data analytics platform

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

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

VariantRetriever is a minimalist package for feature flagging

Data science and numerical computing with Julia

Backend Server for CIViC Project

Structured data processing in Kotlin

ntHash implementation in Rust

Albis: High-Performance File Format for Big Data Systems

WebAssembly modules for genomics

Transcripts annotation and GO enrichment Fisher tests

Nextflow basic tutorial for newbie users

phenol: Phenotype ontology library

A bioinformatics API and web-app to integrate multi-omics datasets & interface with public databases.

SQL Parsers for BigData, built with antlr4.

Bead-based single-cell atac processing

A Snakemake workflow to process single samples or cohorts of paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.

🐞 <3 🐼 A ladybug extension powered by pandas

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

Go data analysis / manipulation library built on top of Apache Arrow

Rust crates for the H3 geospatial indexing system