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

A package for designing compact and comprehensive capture probe sets.

Data intensive science for everyone.

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

A collection of scripts and notes related to genomics and bioinformatics

Official code repository for GATK versions 4 and up

UGENE is free open-source cross-platform bioinformatics software

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

Analysis pipelines for sequencing data

C library for high-throughput sequencing data formats

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

Collection of scripts for bacterial genomics

Ultrafast sequence typing and gene detection from NGS raw reads

pythonic wrapper for htslib

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

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.

Assembling the cause of phenotypes and genotypes from NGS data

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

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

Home of the Genomic Feature and Variation Ontology (GFVO)

Fast and accurate sequence demultiplexing

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

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

Java utilities for Bioinformatics

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

annotate a VCF with other VCFs/BEDs/tabixed files

Tools to process and analyze deep sequencing data.

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

Frequently used commands in bioinformatics

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.

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

A handy variant calling pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Method to optimally select samples for validation and resequencing

A curated list of awesome bioinformatics software.

Tools for analyzing 10X Genomics data

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

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

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

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

Efficient pythonic random access to fasta subsequences

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

A collection of publications on comparison of high-throughput sequencing technologies.

A package for designing activity-informed nucleic acid diagnostics for viruses.

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

highly-efficient & lightweight mutation signature matrix aggregation

Intuitive local web frontend for the BLAST bioinformatics tool

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Rapid large-scale prokaryote pan genome analysis

A tool to circularize genome assemblies

tools for working with genome variation graphs

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

ABRA2

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

NGLess: NGS with less work

Structural variant toolkit for VCFs

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Bayesian genotyper for structural variants

Genomics Extension for SQLite

tools for reading, writing, merging, and remapping SNPs

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

Scalable genomic data analysis.