Artic Field Bioinformatics

Artic is a tool designed for analyzing and creating consensuses from viral nanopore sequencing reads. These also are tied to the use of amplicon schemes (tiled)

Note

This module will output multiple consensuses per barcode of interest. It takes in a raw fastq_pass directory and outputs .vcfs, .fasta, and .bam files for further use

Medaka

Parameters

  • input run folder: directory

    Must contain a fastq_pass directory or a custom inputted one (See below)

  • Primer: option or Directory

    Artic Primer set or a custom one (directory) which contain the genome.fasta and necessary BED file for the primer set

  • Normalize Coverage: Number

  • Barcode Configuration: option

    Which barcode kit you used for demux. Select any for non-barcoded sample

  • FASTQ Dir: Directory, optional

    Select your own custom fastq_pass directory to analyze and demux

  • Medaka Model: option

    FAST or HAC used during basecalling

Returns

  1. Medaka Consensus files: FASTA files containing your consensuses for each barcode

  2. Medaka VCF files: Variant files containing your variant calls for each barcode

  3. Medaka BAM files: BAM files containing your alignment information for each barcode

_images/medaka1.png _images/medaka2.png

Nanopolish

_images/nanopolish1.png _images/nanopolish2.png

Parameters

  • input run folder: directory

    Must contain a fastq_pass directory or a custom inputted one (See below)

  • Primer: option or Directory

    Artic Primer set or a custom one (directory) which contain the genome.fasta and necessary BED file for the primer set

  • Normalize Coverage: Number

  • Barcode Configuration: option

    Which barcode kit you used for demux. Select any for non-barcoded sample

  • FASTQ Dir: Directory, optional

    Select your own custom fastq_pass directory to analyze and demux

  • Sequencing Summary File: File, exists

    Selects the Sequencing summary file in the root of your run directory

    Note

    Oftentimes, this file can be found in the fastq_pass directory. Move it one level up to the root run directory

Returns

  1. Nanopolish Consensus files: FASTA files containing your consensuses for each barcode

  2. Nanopolish VCF files: Variant files containing your variant calls for each barcode

  3. Nanopolish BAM files: BAM files containing your alignment information for each barcode