This repository contains a suite of Common Workflow Language tool wrappers and workflows for processing nanopore sequencing data. Tools and workflows are aimed at the de novo assembly of bacterial genomes, but can also be used for other purposes. Each CWL document contains a description which explains its function. Running tool wrappers or workflows requires a cwl-runner like cwltool.
CWL documents are available for different tasks associated with de novo genome assembly. This is a short introduction to some of the tools/workflows available in the repository.
guppyBasecallingWorkflow.cwl: basecalls regular (1D) reads and creates a single .fastq file containing all reads.
guppy1d2BasecallingWorkflow.cwl: is intended for processing reads created in a 1D² experiment. The workflow produces three fastq files: 1D reads, 1D² reads and a file containing both.
qcatWorkflow: Uses ONT's qcat to demultiplex barcoded reads after basecalling.
deepbinnerWorkflow: Uses Deepbinner to demultiplex basecalled reads after analyzing their raw counterparts (a.k.a. squiggles).
canuTool.cwl: Uses Canu. Trims and corrects reads and creates an assembly using an OLC strategy.
necatWorkflow.cwl: Uses NECAT to correct reads and create an assembly using an OLC strategy.
minasmX3Workflow.cwl: Uses minimap2 to find overlapping regions between reads. [miniasm] will then create a draft assembly based on the overlaps. Three rounds of minimap2 and racon are then used to create a consensus sequence.
medakaTool.cwl: Uses ONT's medaka software to polish a draft assembly where the reads where basecalled with albacore or guppy.
nanopolishWorkflow.cwl: Uses Nanopolish to polish an assembly based on the raw reads (a.k.a. squiggles).
pilonWorkflow.cwl: Uses Pilon to polish a long-read-based draft assembly with short reads (e.g. Illumina reads).
Docker, Singularity or similar software is necessary to execute the tools in the docker containers that are assigned in each tool wrapper. If the execution environment does not support docker containers, tools have to be available locally. Every CWL document references a specific release of a Docker image from this directory. Images are available at Docker Hub. Please consult the Dockerfile to find out which software versions are used in an image.
No installation is needed. Simply dowload a release or clone the repository using the command
git clone https://github.com/ttubb/autopore.git
Relative paths of the repository have to be preserved, otherwise workflows will not find the individual tools.
If you encounter any problems, please open a issue here on GitHub. I am also happy to implement additional tool wrappers or workflows if anybody needs them.