erinyoung/needles

Introduction

erinyoung/needles is a bioinformatics pipeline to download or use a corresponding pre-built poppunk database to use on input fasta files.

The steps are as follows:

1. Download the poppunk database for taxid (https://www.bacpop.org/poppunk/)
2. Assign fasta files to clusters
3. Visualize (microreact is the default)

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.

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

samplesheet.csv:

csv sample,fasta sample1,sample1.fasta

Each row represents a fasta file.

Option 1. Downloading a poppunk database

A list of poppunk databases are in json format at (assets/poppunk*db.json)(./assets/poppunk_db.json). The default taxid is tx:1314 for *Streptococcus pyogenes*.

Current options for taxid:

• "tx:470" : "Acinetobacter baumannii"
• "tx:520" : "Bordetella pertussis"
• "tx:197" : "Campylobacter jejuni"
• "tx:5476" : "Candida albicans"
• "tx:1351" : "Enterococcus faecalis"
• "tx:1352" : "Enterococcus faecium"
• "tx:562" : "Escherichia coli"
• "tx:727" : "Haemophilus influenzae"
• "tx:210" : "Helicobacter pylori"
• "tx:197911" : "Influenza virus"
• "tx:573" : "Klebsiella pneumoniae"
• "tx:446" : "Legionella pneumophila"
• "tx:1639" : "Listeria monocytogenes"
• "tx:36809" : "Mycobacterium abscessus"
• "tx:1773" : "Mycobacterium tuberculosis"
• "tx:485" : "Neisseria gonorrhoeae"
• "tx:487_2" : "Neisseria meningitidis" from "https://doi.org/10.12688/wellcomeopenres.14826.1"
• "tx:487" : "Neisseria meningitidis" from "https://github.com/bacpop/PopPUNK/issues/267"
• "tx:287" : "Pseudomonas aeruginosa"
• "tx:4932" : "Saccharomyces cerevisiae"
• "tx:590" : "Salmonella sp."
• "tx:1280" : "Staphylococcus aureus",
• "tx:40324" : "Stenotrophomonas maltophilia"
• "tx:1311" : "Streptococcus agalactiae"
• "tx:1334" : "Streptococcus dysgalactiae subspecies equisimilis"
• "tx:28037" : "Streptococcus mitis",
• "tx:1313" : "Streptococcus pneumoniae"
• "tx:1314" : "Streptococcus pyogenes"
• "tx:1307" : "Streptococcus suis"

Now, you can run the pipeline using:

bash nextflow run erinyoung/needles \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --taxid <TAXID> \ --outdir <OUTDIR>

Option 2. Using a pre-downloaded poppunk database

bash nextflow run erinyoung/needles \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --db <path/to/poppunk/database/file> \ --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.

Credits

erinyoung/needles was originally written by Erin Young, and is mostly a wrapper for using Poppunk.

Poppunk can be cited with the following paper:

Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Research 29:304-316 (2019). doi:10.1101/gr.241455.118

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.