600 Open source projects that are alternatives of or similar to Awesome Sequencing Tech Papers

Official code repository for GATK versions 4 and up

A package for designing compact and comprehensive capture probe sets.

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

Genomics Extension for SQLite

Analysis pipelines for sequencing data

Antimicrobial Resistance Identification By Assembly

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

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

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

An interactive web tool for quality control of DNA sequencing data

A collection of scripts and notes related to genomics and bioinformatics

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

Assembling the cause of phenotypes and genotypes from NGS data

Data intensive science for everyone.

A tool to circularize genome assemblies

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

Rapid large-scale prokaryote pan genome analysis

Intuitive local web frontend for the BLAST bioinformatics tool

Python and C++ code for reading and writing genomics data.

A faster lmm for GWAS. Supports GPU backend.

Toolkit for preparing genomes for submission to NCBI

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

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

Fast hash function for DNA sequences

highly-efficient & lightweight mutation signature matrix aggregation

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

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

Tools for analyzing 10X Genomics data

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

Multilocus sequence typing by blast using the schemes from PubMLST

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

Bystro genetic analysis (annotation, filtering, statistics)

Provide R access to the NCI Genomic Data Commons portal.

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

Scripts to download genomes from the NCBI FTP servers

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

An open-access bioinformatics text

Compute N50/NG50 and auN/auNG

Fast alignment and preprocessing of chromatin profiles

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

Tools to process and analyze deep sequencing data.

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

A curated list of awesome bioinformatics software.

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

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

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

Earl Grey: A fully automated TE curation and annotation pipeline

De novo assembly based variant calling pipeline for Illumina short reads

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

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.

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

annotate a VCF with other VCFs/BEDs/tabixed files

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

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Example client programs for Saphetor's VarSome annotation API

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

A high-performance, Pythonic language for bioinformatics

The next version of bwa-mem