RSV-AMPSEQ

A nextflow pipeline for genome assembly and variants calling (fusion gene) of human respiratory syncytial virus amplicon sequencing

Usage

Install Nextflow

Install Docker

Running the pipeline:

nextflow run asereewit/rsv_ampseq -r main -latest --input input_samplesheet.csv --output pipeline_output -profile docker

To run it on AWS, add your nextflow config for AWS using -c:

nextflow run asereewit/rsv_ampseq -r main -latest --input input_samplesheet.csv --output pipeline_output -profile docker -with-tower -c nextflow_aws.config

You can create a samplesheet using the bundled python script fastq_dir_samplesheet.py in bin folder, like this:

python fastq_dir_samplesheet.py fastq_dir samplesheet_name.csv

Options

Option	Explanation
--input	samplesheet in csv format with fastq information, samplesheet example: assets/samplesheet.csv
--output	output directory
--skip_fastqc	skip quality control using FastQC (default: false)
--skip_fastp	skip adapters and reads trimming using fastp (default: false)
--trim_len	minimum read length to keep (default:50)
--min_trim_reads	mininum number of trimmed reads required for downstream processes (default: 0)
--min_mapped_reads	minimum number of mapped reads for variants and consensus calling (default: 1000)
--skip_ivar_trim	skip primer clipping step

Custom primers options

Option	Explanation
--ref_RSVA	RSVA reference fasta
--primer_bed_RSVA	RSVA primer bed file with "RSVA" as the header in the first column, "_LEFT" denotes forward primers, "_RIGHT" denotes reverse primers
--ref_gff_RSVA	RSVA gff file with "RSVA" as the header in the first column
--RSVA_F_coord	RSVA reference's fusion gene coordinates in the format of xxxx-yyyy (e.g. 5682-7406)
--RSVA_F_length	RSVA fusion gene length
--ref_RSVB	RSVB reference fasta
--primer_bed_RSVB	RSVB primer bed file with "RSVB" as the header in the first column, "_LEFT" denotes forward primers, "_RIGHT" denotes reverse primers
--ref_gff_RSVB	RSVB gff file with "RSVB" as the header in the first column
--RSVB_F_coord	RSVB reference's fusion gene coordinates in the format of xxxx-yyyy (e.g. 5717-7441)
--RSVB_F_length	RSVB fusion gene length