nCOV19 ANALYSER

nCOV19 Analyser is a customized pipeline for detection of SARS-CoV-2 based on Oxford Nanopore sequencing technology which utilizes the benefits of long reads. nCOV19 Analyser aligns the reads to SARS-CoV-2 reference genome, calls variants, and generates a consensus genome sequence. It then determines lineage, clade and phylogenetic tree information of sample using Pangolin and NextClade. All the information with its data and QC metric files gets summarized in one extensive html report for easy viewing.

FEATURES

  • Built-in Reference Genome for SARS-CoV-2

  • Long Read and High Coverage Sequencing of SARS-CoV-2

  • Map/Align and Variant Calling

  • Consensus Sequence (FASTA) Generation

  • Stats & Plots of Coverage and QC Metrics for Samples

  • Pangolin Lineage Analysis, and NextClade Clade Analysis

  • Nextstrain Phylogenetic Tree Analysis

  • Detailed Excel Reports Generation of Samples

  • Detailed HTML Interactive Report of Samples

  • GISAID Formatted Excel Report Generation

Essential Tool to Add Your Arsenal on the Fight With Covid19!

State-of-the-art Covid19 Specialized Pipeline!

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WORKFLOW

  • Prepare Input Sample(s) Directory

  • Fill Metadata of Samples for Phylogenetic Analysis and GISAID Report

  • Review and Adjust Settings If Desired

TECH SPECS

After Sample Sequencing and Analysis Following Results Are Provided for Each Sample by nCOV19 Analyser:

  • Raw Reads (Fastq format)

  • Consensus Genome Sequence (FNA format)

  • List of SNPs/Indels Compared to NC_045512.2 (VCF format)

  • Avarage Depth

  • Quality Control (Passed/Failed)

  • Pango Lineage

  • WHO Labels for VOI/VOC

  • Cluster Identification with Letter Codes

  • Graphical Illustrations of Statistical Analyzes

  • A Report Page Containing All Summary Informations (HTML format)

  • Alignment File Compared to NC_045512.2 (BAM format)

  • Gene and Amino Acid Based Alteration List

  • Phylogenetic Tree File (JSON format)

  • Consensus Genome Sequence (FASTA format)

KEY OUTPUT FILES

  • vcf.gz

  • consensus.fasta

  • samples_report.xlsx (Contains all the sample stats, linage, clade and QC info)

  • sample.html (Contains report of sample lineage, clade, coverage and N-base coverage stat, detailed amino acid changes and variants, phylogenetic tree file)

  • phylogenetic_tree.json

  • QCmetrics.html

Inside the Software

Optimized for Powerful Analysis

See our recent report

nCOV19 Analyser

State-of-the-art Solution for Covid19!

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See our recent report

Easy to View – One File Format (Excel & Fasta)

Sample Report

GISAID Format

SAMPLE FIGURES

Clade Information

All accessible information about the clade is presented.

Phylogenetic Tree

Samples placed on SARS-CoV-2 phylogeny.

Genome Fraction Coverage

In each depth of coverage, the graph shows percentage of reads that covered in that depth.

x-axis: Coverage (X), y-axis: Fraction of Reference (%)

Mapping Quality Across Reference

Quality of reads mapped to the reference genome.

x-axis: Position (bp), y-axis: Mapping Quality

Genome Coverage Histogram

Coverage distribution of mapped reads.

x-axis: Coverage (X), y-axis: Number of Genomic Locations

Genome Coverage Across Reference

Line plot of coverage for each base across reference genome.

x-axis: Position (bp), y-axis: Coverage (X), GC-Content (%), Mean GC-Content

Mapped Reads GC-Content Distribution

GC-content distribution across the mapped reads.

x-axis: GC-Content (%), y-axis: Fraction of Reads

Duplication Rate Histogram

Duplication rates of each read.

x-axis: Duplication Rate, y-axis: Number of Loci

USER’S MANUAL

Click here to download the user’s manual for nCOV19 Analyser.