Introduction

The AGTC nf-core/champlain is a bioinformatics pipeline for preprocessing of sequencing data coming from the Advanced Genome Technologies Core at UVM. It can handle Singular, Geoxm and Nanopore Data.

1. Demultiplex or Concatenate samples
2. Read QC (FastQC)
3. Present QC for raw reads (MultiQC)

Requirements

You need to have an account in the VACC and also install a conda/mamba environment so that

1. ssh to your VACC account
2. download and install mamba:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" bash Miniforge3-$(uname)-$(uname -m).sh

1. create the mamba environment mamba create -n env_nf nf-core nextflow

2. make sure that you can see /gpfs1/mbsr_tools

Sample Sheet preparation

All sample sheets need to be csv files

• Singular: just use the regular Singular sample sheet used for the instrument
• Nanopore: a Samplesheet with two or more columns, BARCODE and DIRECTORYN. For example: BARCODE,DIRECTORY1,DIRECTORY2,... BARCODE01,/netfiles02/mbsr/AGTC_NANOPORE/etc
  

Usage

Go to the VACC and type:

bash ./champlain.R --instrument TYPE --samplesheet SampleSheet --outputDirectory outputdirectory --directories directories[for Singular]

You can do ./champlain.R --help for help

• Samplesheet: As described above
• Instrument Type: singular, nanopore or geomx
• outputDirectory: where you want the output to go
• datadirectories (only needed for singular): where the fastq data is located.

Pipeline output

The output would go in the output directory as follows:

• demux: demultiplexed fastq (under construction)
• cat: Concatenated data
• fastqc: FASTQC files
• multiqc: MULTIQC output

Credits

nf-core/champlain was originally written by Ramiro Barrantes Reynolds, Ph.D.

We thank the following people for their assistance in the development of this pipeline: Kirsten Tracy, Princess Rodriguez and Stacia Richard.

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #champlain channel (you can join with this invite).

Citations

If you use nf-core/champlain for your analysis, please cite it using the following doi:

"The next-generation sequencing was performed in the Vermont Integrative Genomics Resource Massively Parallel Sequencing Facility and was supported by the University of Vermont Cancer Center, Lake Champlain Cancer Research Organization, UVM College of Agriculture and Life Sciences, and the UVM Larner College of Medicine."

"Sequencing analysis and other bioinformatics services were provided by the Vermont Integrative Genomics Resource DNA Facility and supported by the University of Vermont Larner College of Medicine."

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.