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 fastqdirsamplesheet.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 |