Introduction

nf-core/uno is a bioinformatics pipeline for the co-assembly, binning, and read mapping of mNGS outbreak samples from the The UnO project

Pipeline summary

UnO is an mNGS bioinformatics pipeline that supports The UnO Project. nf-core UnO is the second tier The UnO project which analyzes set of mNGS reads from a well-characterized outbreak. The draft UnO pipeline takes as input outbreak sets of mNGS reads. Reads are co-assembled into a single outbreak assembly and then binned into Metagenomic Assembled Genomes (MAGs). Individual mNGS reads are mapped back to MAGs to identify individual sample contributions. MAGs in common across individual mNGS reads are chosen for further analysis and characterization.

1. Read QC (FastQC)
2. Perform quality and adapter trimming on raw reads (Trimmomatic)
3. Read QC on trimmed reads
4. Co-assemble mNGS reads from outbreak dataset into single outbreak assembly (Megahit)
5. Preparation for binning of metagenomic co-assembly with (Bowtie2). Outbreak co-assembly is used to create an index which individual reads are mapped to determine depth information for downstream binning tools.
6. (MetaBat2) and (MaxBin2) are used to bin MAGs.
7. Perform QC for raw reads (MultiQC)

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

nextflow run nf-core/uno --input /path/to/UnOsamplesheet.csv -profile <conda> -c <CONFIG> --outdir <OUTDIR>

Now, you can run the pipeline using:

nextflow run nf-core/uno \
   -profile <docker/singularity/conda/institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

Current output of the draft UnO output consists of the user specified with following directories: Assembly, FastQC, GenomeBinning, multiqc, pipeline_info, QC_shortreads, and Trimmomatic. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/uno was originally written by Candace Cole.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

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

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

Notices

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