583 Open source projects that are alternatives of or similar to ngs-preprocess

A DSL for data-driven computational pipelines

No description or website provided.

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Short course on reproducible science: what, why, how

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

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rrtools: Tools for Writing Reproducible Research in R

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

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Reproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your personal computer!

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NOTE: This repo is archived. Please see https://github.com/benmarwick/rrtools for my current approach

Open solution to the Google AI Object Detection Challenge 🍁

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Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

Function-oriented Make-like declarative workflows for R

Curated set of transformers that make your work with steppy faster and more effective 🔭

VisTrails is an open-source data analysis and visualization tool. It provides a comprehensive provenance infrastructure that maintains detailed history information about the steps followed and data derived in the course of an exploratory task: VisTrails maintains provenance of data products, of the computational processes that derive these products and their executions.

UGENE is free open-source cross-platform bioinformatics software

Lightweight, Python library for fast and reproducible experimentation 🔬

An R-focused pipeline toolkit for reproducibility and high-performance computing

Fully reproducible, open source scientific articles in LaTeX.

RNA-seq workflow using STAR and DESeq2

ukbREST: efficient and streamlined data access for reproducible research of large biobanks

Package an R workspace and all dependencies as a Docker container

Reproducible Data Science in Python (SciPy 2019 Tutorial)

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A curated list of reproducible research case studies, projects, tutorials, and media

Source code for the CERN Analysis Preservation portal

An automated RNA-seq pipeline using Nextflow

Data intensive science for everyone.

A library for creating and curating reproducible pipelines for scientific and industrial machine learning

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List of IARC bioinformatics nextflow pipelines

Multi-sample somatic variant caller

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

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.

ReproZip is a tool that simplifies the process of creating reproducible experiments from command-line executions, a frequently-used common denominator in computational science.

Example workflows for the drake R package

Short course on the targets R package

An easy-to-use way for running Galaxy workflows.

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A graphical user interface for distributed data processing of high throughput genomics

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A method for circular DNA detection based on probabilistic mapping of ultrashort reads