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

A comprehensive tutorial about GWAS and PRS

📖🔬☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

The next version of bwa-mem

Scripts to download genomes from the NCBI FTP servers

An open source platform for managing and analyzing biomedical big data

highly-efficient & lightweight mutation signature matrix aggregation

Data intensive science for everyone.

A faster lmm for GWAS. Supports GPU backend.

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

Official code repository for GATK versions 4 and up

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

A high-performance, Pythonic language for bioinformatics

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

An interactive web tool for quality control of DNA sequencing data

Toolkit for preparing genomes for submission to NCBI

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

Method to optimally select samples for validation and resequencing

Structural variant toolkit for VCFs

Flexible genotype query among 30,000+ samples whole-genome

GCP Essentials for Bioinformatics Researchers

Bioinformatics library for .NET

Genotyping of segregating mobile elements insertions

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

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

A cool place to store your Hi-C

Earl Grey: A fully automated TE curation and annotation pipeline

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

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

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

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

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

Assembling the cause of phenotypes and genotypes from NGS data

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Ten Quick Tips for Deep Learning in Biology

Reads simulator

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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 open-access bioinformatics text

A powerful open source data warehouse system

Official git repository for Biopython (originally converted from CVS)

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

Compute N50/NG50 and auN/auNG

Bayesian haplotype-based mutation calling

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

Spark VCF data source implementation for Dataframes

Bystro genetic analysis (annotation, filtering, statistics)

simple viewer for variant call format using htslib

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

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

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

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

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

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

nim wrapper for htslib for parsing genomics data files

Collection of scripts for bacterial genomics

Fast hash function for DNA sequences

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

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.