Introduction

ncezid-biome/stylo is a bioinformatics pipeline that can be used to filter, downsample, assemble, and QC ONT longreads. It takes a samplesheet and FASTQ files as input, performs read filtering, downsampling to specified coverage, assembly, and Quality Control (QC).

1. Filters low quality reads (nanoq)
2. Downsamples reads to specific coverage (rasusa)
3. Assembles reads (Flye)
4. Reorients assembly (Dnaapler)
5. Error correction (Dorado polish)
6. QCs assembly (QUAST)

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow.

Note

This pipeline was tested using the following, other versions may work but are currently untested.

nf-core v2.14.1

nextflow v24.04.2

singularity v3.8.7

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

sample,fastq,genus,species,genome_size
sample1,/path/to/sample1.fastq.gz,Salmonella,enterica,-
sample2,/path/to/sample2.fastq.gz,Campylobacter,coli,-
sample3,/path/to/sample3.fastq.gz,Campylobacter,jejuni,-
sample4,/path/to/sample4.fastq.gz,Vibrio,-,-
sample5,/path/to/sample5.fastq.gz,Pseudomonas,aeruginosa,6.0m

Each row represents a fastq file (single-end) with the known genus, species, and genome size.

Note

You can use - where the species is unknown. If the organism is not in the lookup table, you must include a genome size. For more details see full samplesheet description

If you'd like to create your own lookup table see Advanced Usage

Now, you can run the pipeline using:

nextflow run ncezid-biome/stylo \
   -r v1.4.0 \
   -profile singularity \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Note

For CDC users, please see CDC Usage

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 about usage see the Usage Page

Testing stylo on your server

If you'd like to test stylo on your server, you can run the following command

nextflow run ncezid-biome/stylo \
   -r v1.4.0 \
   -profile test,singularity \
   --outdir stylo_test/

Credits

ncezid-biome/stylo was originally written by Arzoo Patel, Mohit Thakur.

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

Justin Kim, Jessica Chen, Peyton Smith, Lee S. Katz, Joe Wirth, Curtis Kapsak

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.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.