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

SAM: Sharpness-Aware Minimization (PyTorch)

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

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Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

A python-based isomiR quantification and analysis pipeline

Scalable long read self-correction and assembly polishing with multiple sequence alignment

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

Utilities for analyzing next generation sequencing data.

A comprehensive tutorial about GWAS and PRS

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Fast hash function for DNA sequences

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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

QP real-time embedded frameworks/RTOS for Arduino (AVR and SAM)

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A set of command line tools based on R and JavaScript.

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

Deep learning infrastructure for bioinformatics

Hands-On Serverless Applications with Go, published by Packt.

PHANOTATE: a tool to annotate phage genomes.

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

A fast whole-genome aligner based on de Bruijn graphs

Bioconductor package for management of multi-assay data

Example client programs for Saphetor's VarSome annotation API

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

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Detection of NCLDV signatures in 'omic data

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

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

calcardbackup: moved to https://codeberg.org/BernieO/calcardbackup

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

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Generic germline variant annotation pipeline

An interactive web portal for exploring immuno-oncology data

A simplified pipeline for ctDNA sequencing data analysis

Explore rearrangements and copy-number amplifications in a cancer genome

PERF is an Exhaustive Repeat Finder

phenol: Phenotype ontology library

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.

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

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Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

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

Tools for working with genomic and high throughput sequencing data.

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

A Suite of Packages for Analysis of Big Genomic Data

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

Precision HLA typing from next-generation sequencing data

Toolkit for preparing genomes for submission to NCBI