TRAPS

Targeted Retrieval and Analysis of Arthopod Borne Pathogen Sequences

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TRAPS is a scalable, highly customizable, and user friendly Nextflow pipeline for hybrid capture sequencing data, enabling detection of infections and coinfections with built in downstream analysis and visual reporting.

Project Overview

Features

• Highly Customizable Configure TRAPS for your use case
• Built In Analyzation Downstream consensus generation, coverage statistics
• Scalable Input as many samples and references as needed
• Sensitive TRAPS analyzes every sample for every reference, ensuring that both infections and coinfections are detected
• Phylogenetic Mapping

Upcoming Features

• Annotation TRAPS transfers annotations from some references to the final output
• Run Management Runs are saved in a custom system using the .tar format
• Mutation Reporting Confidence scoring of amino acid mutations, with an option to add mutations to "flag"
• Reports An interactive web app enables graphical analysis of the data collected

Usage

Quick Start

Requirements:

• Apptainer
• Nextflow

Clone the GitHub Repo:

git clone -b dev https://github.com/henry-j-sommer/TRAPS.git

Navigate to the workflow directory in your new TRAPS folder.

cd TRAPS/workflow

Run the script to build containers

../containers/build-scripts/build-all

It is recommended to store your runs in a dedicated folder. Create a new folder, and remember the name.

Make sure your .FASTQ files are stored in a dedicated directory and follow the formatting guidelines. Make sure your reference configuration file is created.

Configuration

Create your configuration file to edit naming format, tools used, and other parameters.

Warning

Any parameter passed in the CLI will take priority over a configuration file.

Flag	Name	Explanation	Type
--indir	Input Directory	Reads to run	path
--outdir	Output Directory	Output	path
--refs	Reference File	Which references to run against	path
-params-file	Configuration File	A path pointing to your configuration file	path

Running

Run TRAPS with nextflow run main.nf -params-file {params file} within the workflow directory.

Storage

Formatting

FASTQ Filenames

This pipeline expects either single or paired end FASTQ files named using the following format:

{SAMPLEID}_S{NUMBER}_L00{LANE}_R{READ}_001.fastq.gz

References

The references file should be in CSV format. CSV should follow this syntax:

ref_name_external	ref_path
(reference name)	(reference location)

For both formats, the ref_name_external refers to the human readable name of the reference that you want to use to refer to the reference. The ref_path refers to the absolute path to your reference in the FASTA format.

References can be in the .fasta or .gb format.