753 Open source projects that are alternatives of or similar to Vcfanno

Scalable genomic data analysis.

Haplotype VCF comparison tools

Bayesian genotyper for structural variants

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

cython + htslib == fast VCF and BCF processing

GenomeTools genome analysis system.

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

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

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

A collection of scripts and notes related to genomics and bioinformatics

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

De novo assembly based variant calling pipeline for Illumina short reads

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

A powerful open source data warehouse system

🔬 BEDOPS: high-performance genomic feature operations

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

PHANOTATE: a tool to annotate phage genomes.

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

Collection of scripts for bacterial genomics

simple viewer for variant call format using htslib

Earl Grey: A fully automated TE curation and annotation pipeline

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

Spark VCF data source implementation for Dataframes

A faster lmm for GWAS. Supports GPU backend.

A fast 23andMe genome text file parser, now superseded by arv

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

A genome browser that shows long reads and complex variants better

Deep learning infrastructure for bioinformatics

Toolset for SV simulation, comparison and filtering

Fast hash function for DNA sequences

A package for designing compact and comprehensive capture probe sets.

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

Intuitive local web frontend for the BLAST bioinformatics tool

An ultrafast memory-efficient short read aligner

Ten Quick Tips for Deep Learning in Biology

JavaScript VisualizationTools

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

Official git repository for Biopython (originally converted from CVS)

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

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

Reads simulator

Predict plasmids from uncorrected long read data

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

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

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

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

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

Compute N50/NG50 and auN/auNG

Method to optimally select samples for validation and resequencing

Example client programs for Saphetor's VarSome annotation API

Bystro genetic analysis (annotation, filtering, statistics)

Toolkit for preparing genomes for submission to NCBI

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

Assembling the cause of phenotypes and genotypes from NGS data

Fast alignment and preprocessing of chromatin profiles

Genotyping of segregating mobile elements insertions

Provide R access to the NCI Genomic Data Commons portal.

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

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

Home of the Genomic Feature and Variation Ontology (GFVO)