BonoboFlow

B O N O B O F L O W - P I P E L I N E

The BonoboFlow pipeline is a dedicated tool developed for the precise execution of viral genome assembly and haplotypes construction from MinION sequencing reads

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                          BonoboFlow  ~  version 1.0
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Introduction

BonoboFlow is a nextflow pipeline for reproducible and precise execution of viral genome assembly and haplotypes construction

Installation

BonoboFlow requires: nextflow (version 22.10.4) docker singularity

We recommend to install the packages as follow

git clone https://github.com/nchis09/BonoboFlow.git
cd BonoboFlow-main/packages/RATTLE
./build.sh
conda create -n nextflow -c bioconda -c conda-forge openjdk=11.0.8 nextflow python
conda activate nextflow

Note: make sure docker has at least 60GB available disk space, 6CPUS, 16GB memory

cd ../../
nextflow run bonoboflow.nf --help

Usage

The pipeline takes in the fast5 file from Nanopore sequencing technology

conda activate nextflow

nextflow run BonoboFlow.nf -resume --in_fastq <in put directory> --outfile <output directory> --ref_genome <reference genone.fasta> --lowerlength 1000 --upperlength 5000 -w <work directory> --sample_id <sample_id.csv> --kit <sequencing kit>  --flowcell <flow cell used during sequencing> 

    

    Mandatory arguments:
      --in_fastq                  Path to input fastq dirctory 
      --outfile                   Path to output directory
      --ref_genome                reference sequence
      --sample_id                 a csv file containing barcode_Ids and sample Ids

    Other arguments:
      --barcods                   barcods used during sequencing. The default 
                                  barcoding kits are "EXP-NBD104 EXP-NBD114"
      --cpu                       cpus to used during the analyis. default is 8
      --lowerlength               set the lower length for input reads filter (default: 1000)
      --upperlength               set the upper length for input reads filter (default: 20000)
      --cpu                       CPUs to be used during the analysis. The default is 8
      --memory                    Memory allocated for each process. The default is 30 GB
      --lowerlength               Set the lower length for input reads filter (default: 1000)
      --upperlength               Set the upper length for input reads filter (default: 10000)
      --pipeline                  Specify whether you want to do genome assembly or generate haplotype. The default is assembly
      --genomesize                Only required if you are running genome assembly (default: 5k)

Profiles

BonoboFlow can be run under different computing environments, simply choose an appropriate profile via the -profile argument. Could take only -profile docker

Pipeline

Output fiiles

• consensus*.fasta: FASTA files of consensus sequences - one per sample

Pipeline information output

• Bonoboflow_DAG.html: Graphical representation of the pipeline's processes/operators and channels between them.

input Parameters

Mandatory parameters

• --in_fastq : Path to input fastq dirctory
• --sample_id: a csv file containing barcode_Ids and sample Ids
• --ref_genome: reference sequence

Optional parameters

• --barcods: barcods used during sequencing. The default barcoding kits are "EXP-NBD104 EXP-NBD114"
• --cpu: cpus to used during the analyis. default is 8
• --lowerlength: set the lower length for input reads filter (default: 150)
• --upperlength: set the upper length for input reads filter (default: 100,000)

Output parameters

Mandatory parameters

• --outfile: Path to output directory

Troubleshooting

Kindly report any issues at https://github.com/nchis09/BonoboFlow/issues

License

BonoboFlow is licensed under GNU GPL v3.

Citation

This work is currently under peer review. A formal citation will be availed in due course.

BonoboFlow