569 Open source projects that are alternatives of or similar to Hts Nim

Earl Grey: A fully automated TE curation and annotation pipeline

A fast whole-genome aligner based on de Bruijn graphs

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

NGLess: NGS with less work

Official code repository for GATK versions 4 and up

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

The next version of bwa-mem

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

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

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

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

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GenomeTools genome analysis system.

A genome browser that shows long reads and complex variants better

A powerful open source data warehouse system

Deep learning infrastructure for bioinformatics

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Proof-of-concept seq-to-graph mapper and graph generator

cython + htslib == fast VCF and BCF processing

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Model and predict short DNA sequence features with neural networks

Haplotype VCF comparison tools

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

JavaScript VisualizationTools

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

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

De novo assembly based variant calling pipeline for Illumina short reads

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

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Compute N50/NG50 and auN/auNG

Analysis pipelines for sequencing data

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

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A package for designing compact and comprehensive capture probe sets.

Fast hash function for DNA sequences

A high-performance, Pythonic language for bioinformatics

Data intensive science for everyone.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

GO enrichment with python -- pandas meets networkx

MyGene.info: A BioThings API for gene annotations

dna2vec: Consistent vector representations of variable-length k-mers

Simulate genealogical trees and genomic sequence data using population genetic models

Biological sequences for the julia language

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

Provides access to complex Bioinformatics software (even BioLinux!) in just one command.

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

Robust and efficient workflows using a simple language agnostic approach

pymzML - an interface between Python and mzML Mass spectrometry Files

The START App: R Shiny Transcriptome Analysis Resource Tool

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Solutions to assignments of Coursera Specializations - Deep learning, Machine learning, Algorithms & Data Structures, Image Processing and Python For Everybody

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Demonstrating best practices for bioinformatics command line tools

Global Biotic Interactions provides access to existing species interaction datasets

Simple simulation of single-cell RNA sequencing data