461 Open source projects that are alternatives of or similar to Htsjdk

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

ABRA2

Tools to process and analyze deep sequencing data.

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

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

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

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

Scalable genomic data analysis.

Multilocus sequence typing by blast using the schemes from PubMLST

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

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

tools for working with genome variation graphs

Assembling the cause of phenotypes and genotypes from NGS data

cython + htslib == fast VCF and BCF processing

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

annotate a VCF with other VCFs/BEDs/tabixed files

Java utilities for Bioinformatics

Spark VCF data source implementation for Dataframes

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

highly-efficient & lightweight mutation signature matrix aggregation

De novo assembly from Oxford Nanopore reads.

An open-source toolkit for large-scale genomic analysis

Sequana: a set of Snakemake NGS pipelines

GenomeTools genome analysis system.

RNA-seq workflow using STAR and DESeq2

Inference of ploidy and heterozygosity structure using whole genome sequencing data

AQUAS TF and histone ChIP-seq pipeline

Viral genomics analysis pipelines

GCP Essentials for Bioinformatics Researchers

Graph realignment tools for structural variants

A Python library for creating and manipulating musical patterns, designed for use in algorithmic composition, generative music and sonification. Can be used to generate MIDI events, MIDI files, OSC messages, or custom events.

A genome browser that shows long reads and complex variants better

Tools to work with variant call format files

Bioinformatics library for .NET

R package for analyzing single-cell RNA-seq data

Airline Booking is a sample web application that provides Flight Search, Flight Payment, Flight Booking and Loyalty points including end-to-end testing, GraphQL and CI/CD. This web application was the theme of Build on Serverless Season 2 on AWS Twitch running from April 24th until end of August in 2019.

Polyrhythmic Sequencer library for Web Audio API.

A collection of Galaxy-related training material

structural variant calling and genotyping with existing tools, but, smoothly.

Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features

Genomic Data Retrieval with R

Script to automatically create and run IGV snapshot batchscripts

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

SDK for GPU accelerated genome assembly and analysis

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Chromosome visualization for the web

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

Pan-genome wide association studies

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

Deep learning infrastructure for bioinformatics

A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

Learning the Sequence Alignment/Map format

This repo contains all the SAM templates created in the Twitch series #SessionsWithSAM. The show is every Thursday on Twitch at 10 AM PDT.

A fast whole-genome aligner based on de Bruijn graphs

Sampler, Sequencer, Multi-engine synth and effects - in a box! [WIP]

Analysis Pipeline for Single Cell ATAC-seq

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

Discovering known and novel miRNAs from small RNA sequencing data

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads