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nCOV 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.
Inside the Software
Easy to View – One File Format (Excel & Fasta)
WORKFLOW
SAMPLE FIGURES
Phylogenetic Tree
CNV Diagram
The diagram shows chromosome based copy number variants. While dark blue denotes loss, dark red denotes gain.
Mapping Quality Across Reference
Quality of reads mapped to the reference genome.
Geonome Coverage Histogram
Coverage distribution of mapped reads.
Genome Coverage Across Reference
Line plot of coverage for each base across reference genome.
Mapped Reads GC-Content Distribution
GC-content distribution across the mapped reads.
Duplication Rate Histogram
Duplication rates of each read.
Features
Built-in Reference Genome for SARS-CoV-2
Long Read and High Coverage Sequencing of SARS-CoV-2
Map/Align and Variant Calling
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
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)
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)
Pango Lineage
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