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

Genetic Map Comparison

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

A Python platform for Structural Bioinformatics

Demonstrating best practices for bioinformatics command line tools

Method to optimally select samples for validation and resequencing

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

The uncompromising Snakemake code formatter

Exact Tandem Repeat Finder (not a TRF replacement)

Sample search by metadata and features

Simple simulation of single-cell RNA sequencing data

A D library for computational biology and bioinformatics

A curated list of resources for machine learning for small-molecule drug discovery

Unix, R and python tools for genomics and data science

(WIP) best-practices workflow for rare disease

🌈Scaffold genome sequence assemblies using linked read sequencing data

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

List of Computer Science courses with video lectures.

Bioinformatics Workbook repository

GeneValidator: Identify problems with predicted genes

WebLogo 3: Sequence Logos redrawn

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

A friendly next-generation interface for Genomic data discovery powered by InterMine

Complex structural variant detection from WGS data

BWK awk modified for biological data

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

API for linked biological knowledge

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

Genome inference from a population reference graph

Golang for Bioinformatics

MMseqs2: ultra fast and sensitive search and clustering suite

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

Structural variant toolkit for VCFs

MetaSRA: normalized sample-specific metadata for the Sequence Read Archive

The Microbiome Interpretable Temporal Rule Engine

A DSL for data-driven computational pipelines

d3 library to build circular graphs

LAMBDA – the Local Aligner for Massive Biological DatA

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Bioinformatics containers

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Improving genome bins through the combination of different binning programs

Python library to handle Gene Ontology (GO) terms

📊 Codon usage tables in code-friendly format + Python bindings

DOM Text Based Multiple Sequence Alignment Library

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

Tools for working with SAM/BAM data

FastQC port to Qt5: A quality control tool for high throughput sequence data.

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

A simplified pipeline for ctDNA sequencing data analysis

MMseqs2 app to run on your workstation or servers

Script to automatically create and run IGV snapshot batchscripts

Comprehensive toolkit for generating various numerical features of protein sequences

De novo genome assembly and multisample variant calling

Phylogenetic trees in Julia

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

The Ontology for Biomedical Investigations

Application for making ENCODE Blacklists