Skip to content
master
Go to file
Code

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

README.md

insdc-pipeline

A Snakemake pipeline to run analyses on public genome assemblies for visualisation in the BlobToolKit Viewer

DOI

While designed for use on public genome assemblies and read files, this pipeline is also suitable for use with local assembly and read files. If the assembly and read files exist locally in the working directory when the pipeline is run, the remote fetches will be skipped.

More information and tutorials are available at blobtoolkit.genomehubs.org/pipeline/

Overview

The final output of this pipeline is a BlobDir dataset directory containing a set of JSON files ready for interactive visualisation with the BlobToolKit Viewer (Figure 1).

Figure 1

The pipeline (Figure 2) is implemented using Snakemake and will fetch all required database and assembly files then run BLAST/Diamond similarity searches and bwa/minimap2 read mapping and for processing with BlobTools.

Figure 2

Installation

Installation instructions for all BlobToolKit components have moved to blobtoolkit.genomehubs.org/install

Usage

Information on pipeline configuration and running has been moved to blobtoolkit.genomehubs.org/pipeline/pipeline-tutorials

Format specification

The BlobDir output of this pipeline contains a set of JSON files and can be validated using the associated JSON-schema. A complete specification and validator for the BlobDir format are available at github.com/blobtoolkit/specification.

About

SnakeMake pipeline to run BlobTools on public assemblies

Resources

License

Packages

No packages published
You can’t perform that action at this time.