PoSeCo | Poliovirus Sequencing Consortium
piranha | Poliovirus Investigation Resource Automating Nanopore Haplotype Analysis

Sequencing report: MIN001 2023-10-30


User | Áine O'Toole

Institute | Institute of Ecology and Evolution

This report is generated by piranha, a software tool developed to help standardise and streamline the analysis of poliovirus sequencing reads. It has been developed by members of the Rambaut group at the University of Edinburgh as part of the Poliovirus Sequencing Consortium. If you have used piranha in your work, please cite the software.



Table 1 | Sample summary information

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Sample Barcode Sample Classification Reference Group Number Of Mutations Sequence (VP1)
Sample01 barcode01 Sabin-like Sabin3-related 8 Download FASTA
Sample01 barcode01 Sabin-like Sabin2-related 1 Download FASTA
Sample02 barcode02 VDPV Sabin2-related 10 Download FASTA
Sample04 barcode04 Sabin-like Sabin3-related 8 Download FASTA
Sample05 barcode07 Sabin-like Sabin2-related 1 Download FASTA
Sample05 barcode07 Sabin-like Sabin3-related 1 Download FASTA
Sample06 barcode09 VDPV Sabin1-related 50 Download FASTA

Table 2 | Composition of samples

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Sample Barcode Sabin1-Related Sabin2-Related Sabin3-Related Wpv1 Wpv2 Wpv3 Nonpolioev Unmapped
Sample01 barcode01 0 245 238 0 0 0 0 14
Sample02 barcode02 0 707 0 0 0 0 0 39
Sample03 barcode03 0 1 3 17 0 0 1 175
Sample04 barcode04 0 0 238 0 0 0 0 12
Sample05 barcode07 0 137 338 1 0 0 34 122
Sample06 barcode09 1164 0 0 0 0 0 0 2350

Table 3 | Flagged samples

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Identical sequences Sequence IDs
1 Sample01|Sabin3-related|CNS1|EDI001|2022-01-01
Sample04|Sabin3-related|CNS1|LON002|2022-01-05
2 Sample01|Sabin2-related|CNS1|EDI001|2022-01-01
Sample05|Sabin2-related|CNS1|EDI003|2022-03-01

Table 4 | Controls

Pass Sample Barcode Sabin1-Related Sabin2-Related Sabin3-Related Wpv1 Wpv2 Wpv3 Nonpolioev Unmapped
negative1 barcode05 0 0 5 0 0 0 0 0
positive barcode06 0 0 5 0 0 0 0 0
negative2 barcode08 0 0 0 0 0 0 0 0

Figure 1 | Barcodes location on 96-well plate


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Figure 2 | Sabin3-related phylogeny

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Figure 3 | Sabin2-related phylogeny

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Figure 4 | Sabin1-related phylogeny


Table 5 | Configuration settings

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Configuration option Value
min_read_length 1000
max_read_length 1300
min_map_quality 50
min_read_depth 50
min_aln_block 600
min_read_pcent 10.0
medaka_model r941_min_hac_variant_g507
primer_length 30
analysis_mode vp1
run_phylo True

General citation for Piranha

O’Toole Á, Colquhoun R, Ansley C, Troman C, Maloney D, Vance Z, Akello J, Bujaki E, Majumdar M, Khurshid A, Arshad Y, Alam MM, Martin J, Shaw A, Grassly N, Rambaut A (2023) Automated detection and classification of polioviruses from nanopore sequencing reads using piranha. bioRxiv https://doi.org/10.1101/2023.09.05.556319