FINDER

FINDER is a library/docker container for a pipeline performing: Downloading of SRA/DRA/ERA data, Quality control, Alignment with reference and optionally Assembly by reference creating Metagenomic assembled genomes. This tool is intended to work alongside blast screening to determine whether or not a reference sequence appears within metagenomic data. If so how much? But can be used similarly to blast to give a coverage of a reference sequence.

Tools Used

• Retrieval of FASTQ files and corresponding metadata and reference genomes from NCBI, using fasterq-dump
• Quality control and trimming with Cutadapt, FastQC and MultiQC.
• Alignment created using Bowtie between the reference and raw data.
• SAMtools to create coverage tables of the reference, then calculating the breadth of coverage found at atleast 1X depth. - Can be changed in bowtiecoverage(2).sh files.
• SPAdes to create an Metagenomic Assembled Genome using the aligned sequences from Bowtie2 alongside De Novo methods.
• Quast to look at the quality and accuracy and to perform a comparison against the reference, producing a report.

Installation

For this package you can easily run it on a local machine or a Google Cloud web service. First Installation takes a while through Docker as it is having to compile all the code needed (around 10-20mins)

Local Machine

Prerequisites

Before you continue, ensure you have met the following requirements:

• You have installed Docker for your operating system.
• If you are on windows then you will also need WSL.

git clone https://github.com/keith-harrison/FINDER/
cd FINDER
docker-compose up 

• Access website at localhost:80
• instructions detailed on website and files saved to localhost/program

Google Cloud Setup

Before you continue, ensure you have met the following requirements:

• Google Cloud Account with Credit on (~£0.077/hour when being fully used for 24 hours, so shutdown when not in use of processing)
• Create the VM instance with information below and SSH performing the code below.
• Changing boot disk options using Container Optimized Machine OS, e2-standard-2 as with ~75GB+ of storage and allow HTTP traffic, May be better to look for a cheap 16GB instance for assembly.

#There are some issues with permissions so chmod is needed
#Can take sometime to setup on first try (around 15-20mins) as all dependencies are downloaded and compiled.
git clone https://github.com/keith-harrison/FINDER/
chmod -R 777 FINDER 
cd FINDER
docker run --rm -v /var/run/docker.sock:/var/run/docker.sock -v "$PWD:$PWD" -w="$PWD" docker/compose:1.24.0 up

• Access website at ip given on VM instance page externalip:80
• instructions detailed on website and files can be accessed on externalip/program

Downloading Results

Results can be easily downloaded to another machine using the code below in the command terminal.

wget --recursive --no-clobber --page-requisites --html-extension --convert-links ipaddress/program

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update tests as appropriate.