assembleBAC-ONT

Introduction

avantonder/assembleBAC-ONT is a bioinformatics pipeline that de novo assembles and annotates Oxford Nanopore (ONT) long-read sequence data.

1. Aggregate pre-demultiplexed reads from MinKNOW/Guppy (artic guppyplex)
2. Filter long reads (Filtlong)
3. Downsample fastq files (Rasusa)
4. Remove adapter sequences (Porechop)
5. de novo assembly (Flye)
6. Polish assemblies with ONT data (Medaka)
7. Assembly metrics (Quast)
8. Assembly completeness (CheckM2)
9. Sequence Type assignment (mlst)
10. Annotation (Bakta)
11. Present QC, visualisation and custom reporting for filtering and assembly results (MultiQC)

Quick Start

1. Install nextflow(>=23.04.0)

2. Install any of Docker, Singularity, Podman, Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs)

3. Download the Bakta light database (Bakta is required to run the amrfinder_update command):

   wget https://zenodo.org/record/7669534/files/db-light.tar.gz
   tar -xzf db-light.tar.gz
   rm db-light.tar.gz
   amrfinder_update --force_update --database db-light/amrfinderplus-db/

4. Download the CheckM2 database (CheckM2 is required):

   checkm2 database --download --path path/to/checkm2db

5. Start running your own analysis!

   • Typical command for assembly and annotation

   nextflow run avantonder/assembleBAC-ONT \
       -profile singularity \
       -c <INSTITUTION>.config \
       --input samplesheet.csv \
       --fastq_dir path/to/fastq/files \
       --genome_size <ESTIMATED GENOME SIZE e.g. 4M> \
       --medaka_model <MEDAKA MODEL> \
       --min_read_length <MINIMUM READ LENGTH> \
       --outdir <OUTDIR> \
       --baktadb path/to/baktadb/dir \
       --checkm2db path/to/checkm2db/dir/uniref100.KO.1.dmnd \
       -resume

See usage docs for all of the available options when running the pipeline.

Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (<INSTITUTION>.config in the example command above). You can chain multiple config profiles in a comma-separated string.

• The pipeline comes with config profiles called docker, singularity, podman, shifter, charliecloud and conda which instruct the pipeline to use the named tool for software management. For example, -profile test,docker.
• Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.
• If you are using singularity, please use the nf-core download command to download images first, before running the pipeline. Setting the NXF_SINGULARITY_CACHEDIR or singularity.cacheDir Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
• If you are using conda, it is highly recommended to use the NXF_CONDA_CACHEDIR or conda.cacheDir settings to store the environments in a central location for future pipeline runs.

Documentation

The avantonder/assembleBAC-ONT pipeline comes with documentation about the pipeline usage, parameters and output.

Credits

avantonder/assembleBAC-ONT was originally written by Andries van Tonder. I wouldn't have been able to write this pipeline with out the tools, documentation, pipelines and modules made available by the fantastic nf-core community. In particular, the excellent viralrecon pipeline was a source of code and inspiration. Finally, a shout out to Robert Petit's Dragonflye as an additional source of inspiration.

Feedback

If you have any issues, questions or suggestions for improving assembleBAC-ONT, please submit them to the Issue Tracker.

Citations

If you use the avantonder/assembleBAC-ONT pipeline, please cite it using the following doi: ZENODO_DOI

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.