Mapping of reads to selected viruses in DAMIAN results (version 2)

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Tags: pipeline

RV4_DNA_on_HSV-2_strain_G_OM370995

  1. Prepare input raw data

    1. # -- Ringversuch --
    2. ~/DATA/Data_Damian/241213_VH00358_120_AAG523FM5_Ringversuch
    3. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20579/01_RV1_DNA_S1_R1_001.fastq.gz RV1_DNA_R1.fastq.gz
    4. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20579/01_RV1_DNA_S1_R2_001.fastq.gz RV1_DNA_R2.fastq.gz
    5. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20580/02_RV2_DNA_S2_R1_001.fastq.gz RV2_DNA_R1.fastq.gz
    6. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20580/02_RV2_DNA_S2_R2_001.fastq.gz RV2_DNA_R2.fastq.gz
    7. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20581/03_RV3_DNA_S3_R1_001.fastq.gz RV3_DNA_R1.fastq.gz
    8. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20581/03_RV3_DNA_S3_R2_001.fastq.gz RV3_DNA_R2.fastq.gz
    9. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20582/04_RV4_DNA_S4_R1_001.fastq.gz RV4_DNA_R1.fastq.gz
    10. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20582/04_RV4_DNA_S4_R2_001.fastq.gz RV4_DNA_R2.fastq.gz
    11. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20583/05_RV5_DNA_S5_R1_001.fastq.gz RV5_DNA_R1.fastq.gz
    12. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20583/05_RV5_DNA_S5_R2_001.fastq.gz RV5_DNA_R2.fastq.gz
    13. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20584/06_RV6_DNA_S6_R1_001.fastq.gz RV6_DNA_R1.fastq.gz
    14. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20584/06_RV6_DNA_S6_R2_001.fastq.gz RV6_DNA_R2.fastq.gz
    15. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20585/07_RV1_RNA_S7_R1_001.fastq.gz RV1_RNA_R1.fastq.gz
    16. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20585/07_RV1_RNA_S7_R2_001.fastq.gz RV1_RNA_R2.fastq.gz
    17. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20586/08_RV2_RNA_S8_R1_001.fastq.gz RV2_RNA_R1.fastq.gz
    18. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20586/08_RV2_RNA_S8_R2_001.fastq.gz RV2_RNA_R2.fastq.gz
    19. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20587/09_RV3_RNA_S9_R1_001.fastq.gz RV3_RNA_R1.fastq.gz
    20. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20587/09_RV3_RNA_S9_R2_001.fastq.gz RV3_RNA_R2.fastq.gz
    21. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20588/10_RV4_RNA_S10_R1_001.fastq.gz RV4_RNA_R1.fastq.gz
    22. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20588/10_RV4_RNA_S10_R2_001.fastq.gz RV4_RNA_R2.fastq.gz
    23. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20589/11_RV5_RNA_S11_R1_001.fastq.gz RV5_RNA_R1.fastq.gz
    24. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20589/11_RV5_RNA_S11_R2_001.fastq.gz RV5_RNA_R2.fastq.gz
    25. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20590/12_RV6_RNA_S12_R1_001.fastq.gz RV6_RNA_R1.fastq.gz
    26. ln ../241213_VH00358_120_AAG523FM5_Ringversuch/p20590/12_RV6_RNA_S12_R2_001.fastq.gz RV6_RNA_R2.fastq.gz

  2. Prepare virus database and select 8 representatives for the eight given viruses from the database

    1. # -- Download all genomes --
    2. # enterovirus D68
    3. # HSV-1
    4. # HSV-2
    5. # Influenza A H1N1
    6. # Cytomegalovirus AD169 (The genome size of Human herpesvirus 5 (HHV-5) — more commonly known as Cytomegalovirus (CMV))
    7. # Influenza A H3N2
    8. # Monkeypox
    9. # HIV-1
    11. esearch -db nucleotide -query "txid42789[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_42789_ncbi.fasta
    12. python ~/Scripts/filter_fasta.py genome_42789_ncbi.fasta complete_42789_ncbi.fasta    #899
    13. esearch -db nucleotide -query "txid10298[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10298_ncbi.fasta
    14. python ~/Scripts/filter_fasta.py genome_10298_ncbi.fasta complete_10298_ncbi.fasta    #162
    15. esearch -db nucleotide -query "txid10310[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10310_ncbi.fasta
    16. python ~/Scripts/filter_fasta.py genome_10310_ncbi.fasta complete_10310_ncbi.fasta    #33
    17. esearch -db nucleotide -query "txid1323429[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_1323429_ncbi.fasta
    18. python ~/Scripts/filter_fasta2.py genome_1323429_ncbi.fasta complete_1323429_ncbi.fasta    #465
    19. esearch -db nucleotide -query "txid10360[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10360_ncbi.fasta
    20. python ~/Scripts/filter_fasta2.py genome_10360_ncbi.fasta complete_10360_ncbi.fasta    #1
    21. esearch -db nucleotide -query "txid41857[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_41857_ncbi.fasta
    22. python ~/Scripts/filter_fasta2.py genome_41857_ncbi.fasta complete_41857_ncbi.fasta    #120
    23. esearch -db nucleotide -query "txid10244[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_10244_ncbi.fasta
    24. python ~/Scripts/filter_fasta.py genome_10244_ncbi.fasta complete_10244_ncbi.fasta    #2525
    25. esearch -db nucleotide -query "txid11676[Organism:exp]" | efetch -format fasta -email j.huang@uke.de > genome_11676_ncbi.fasta
    26. python ~/Scripts/filter_fasta.py genome_11676_ncbi.fasta complete_11676_ncbi.fasta    #485995-->7416
    28. # ---- Alternatively, using ENA instead to download the genomes ----
    29. # https://www.ebi.ac.uk/ena/browser/view/11676 (1138065 records)
    30. # #Click "Sequence" and download "Counts" (1132648) and "Taxon descendants count" (1138065) if there is enough time! Downloading time points is 09.04.2025.
    31. # python ~/Scripts/filter_fasta.py  ena_11676_sequence.fasta complete_11676_ena.fasta  #1138065-->????
    33. # Virus Name    NCBI TaxID
    34. # ------------------------
    35. # Enterovirus D68   42789                             >PQ895337.1 Enterovirus D68 isolate SH2024-25870
    36. # HSV-1 (Herpes Simplex Virus 1)    10298             >PQ569920.1 Human alphaherpesvirus 1 isolate MacIntyre, complete genome
    37. # HSV-2 (Herpes Simplex Virus 2)    10310             >OM370995.1 Human alphaherpesvirus 2 strain G, complete genome
    39.     samtools faidx complete_42789_ncbi.fasta PQ895337.1 > Enterovirus_D68_isolate_SH2024-25870.fasta
    40.     samtools faidx complete_10298_ncbi.fasta PQ569920.1 > HSV-1_isolate_MacIntyre.fasta
    41.     samtools faidx complete_10310_ncbi.fasta OM370995.1 > HSV-2_strain_G.fasta
    43. # Influenza A virus (H1N1)  1323429
    44. # The Influenza A virus (H1N1) genome is composed of eight single-stranded negative-sense RNA segments, and the total genome size is approximately 13,500 nucleotides (13.5 kb).
    45. # Segment   Gene    Protein Product(s)  Approx. Length (nt)
    46. # 1 PB2 Polymerase basic 2  ~2,341
    47. # 2 PB1 Polymerase basic 1, PB1-F2  ~2,341
    48. # 3 PA  Polymerase acidic   ~2,233
    49. # 4 HA  Hemagglutinin   ~1,778
    50. # 5 NP  Nucleoprotein   ~1,565
    51. # 6 NA  Neuraminidase   ~1,413
    52. # 7 M   Matrix proteins (M1, M2)    ~1,027
    53. # 8 NS  Nonstructural (NS1, NS2)    ~890
    55. # >LC662544.1 Influenza A virus (H1N1) A/PR/8/34 NEP, NS1 genes for nonstructural protein 2, nonstructural protein 1, complete cds
    56. # >LC662543.1 Influenza A virus (H1N1) A/PR/8/34 M2, M1 genes for matrix protein 2, matrix protein 1, complete cds
    57. # >LC662542.1 Influenza A virus (H1N1) A/PR/8/34 NA gene for neuraminidase, complete cds
    58. # >LC662541.1 Influenza A virus (H1N1) A/PR/8/34 NP gene for nucleoprotein, complete cds
    59. # >LC662540.1 Influenza A virus (H1N1) A/PR/8/34 HA gene for haemagglutinin, complete cds
    60. # >LC662539.1 Influenza A virus (H1N1) A/PR/8/34 PA, PA-X genes for polymerase PA, PA-X protein, complete cds
    61. # >LC662538.1 Influenza A virus (H1N1) A/PR/8/34 PB1, PB1-F2 genes for polymerase PB1, PB1-F2 protein, complete cds
    62. # >LC662537.1 Influenza A virus (H1N1) A/PR/8/34 PB2 gene for polymerase PB2, complete cds
    64.     samtools faidx complete_1323429_ncbi.fasta LC662537.1 > H1N1_A-PR-8-34_PB2.fasta
    65.     samtools faidx complete_1323429_ncbi.fasta LC662538.1 > H1N1_A-PR-8-34_PB1.fasta
    66.     samtools faidx complete_1323429_ncbi.fasta LC662539.1 > H1N1_A-PR-8-34_PA.fasta
    67.     samtools faidx complete_1323429_ncbi.fasta LC662540.1 > H1N1_A-PR-8-34_HA.fasta
    68.     samtools faidx complete_1323429_ncbi.fasta LC662541.1 > H1N1_A-PR-8-34_NP.fasta
    69.     samtools faidx complete_1323429_ncbi.fasta LC662542.1 > H1N1_A-PR-8-34_NA.fasta
    70.     samtools faidx complete_1323429_ncbi.fasta LC662543.1 > H1N1_A-PR-8-34_M.fasta
    71.     samtools faidx complete_1323429_ncbi.fasta LC662544.1 > H1N1_A-PR-8-34_NS.fasta
    73. # Human cytomegalovirus AD169   10360
    75. # Influenza A virus (H3N2)  41857
    77. # >LC817411.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 8, complete sequence
    78. # >LC817410.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 7, complete sequence
    79. # >LC817409.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 6, complete sequence
    80. # >LC817408.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 5, complete sequence
    81. # >LC817407.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 4, complete sequence
    82. # >LC817406.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 3, complete sequence
    83. # >LC817405.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 2, complete sequence
    84. # >LC817404.1 Influenza A virus H3N2 A_Fukushima_OR808_2023 RNA, seqment 1, complete sequence
    86.     samtools faidx complete_41857_ncbi.fasta LC817404.1 > H3N2_A-Fukushima-OR808-2023_PB2.fasta
    87.     samtools faidx complete_41857_ncbi.fasta LC817405.1 > H3N2_A-Fukushima-OR808-2023_PB1.fasta
    88.     samtools faidx complete_41857_ncbi.fasta LC817406.1 > H3N2_A-Fukushima-OR808-2023_PA.fasta
    89.     samtools faidx complete_41857_ncbi.fasta LC817407.1 > H3N2_A-Fukushima-OR808-2023_HA.fasta
    90.     samtools faidx complete_41857_ncbi.fasta LC817408.1 > H3N2_A-Fukushima-OR808-2023_NP.fasta
    91.     samtools faidx complete_41857_ncbi.fasta LC817409.1 > H3N2_A-Fukushima-OR808-2023_NA.fasta
    92.     samtools faidx complete_41857_ncbi.fasta LC817410.1 > H3N2_A-Fukushima-OR808-2023_M.fasta
    93.     samtools faidx complete_41857_ncbi.fasta LC817411.1 > H3N2_A-Fukushima-OR808-2023_NS.fasta
    95. # Monkeypox virus   10244: >OP689666.1 Monkeypox virus isolate MPXV/Germany/2022/RKI513, complete genome
    96.     samtools faidx complete_10244_ncbi.fasta OP689666.1 > Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta
    98. # Human immunodeficiency virus 1    11676: >AJ866558.1 Human immunodeficiency virus 1 complete genome, isolate 01IC-PCI127
    99.     samtools faidx complete_11676_ncbi.fasta AJ866558.1 >  HIV-1_isolate_01IC-PCI127.fasta
    101. # -- Selected genomes saved in the fasta-files --
    102. # Enterovirus_D68_isolate_SH2024-25870.fasta (7391 nt)
    103. # HSV-1_isolate_MacIntyre.fasta (151817 nt)
    104. # HSV-2_strain_G.fasta (155498 nt)
    105. # H1N1_A-PR-8-34_PB2.fasta (2341 nt)
    106. # H1N1_A-PR-8-34_PB1.fasta (2341 nt)
    107. # H1N1_A-PR-8-34_PA.fasta (2233 nt)
    108. # H1N1_A-PR-8-34_HA.fasta (1775 nt)
    109. # H1N1_A-PR-8-34_NP.fasta (1565 nt)
    110. # H1N1_A-PR-8-34_NA.fasta (1413 nt)
    111. # H1N1_A-PR-8-34_M.fasta (1027 nt)
    112. # H1N1_A-PR-8-34_NS.fasta (890 nt)
    113. # Human_cytomegalovirus_strain_AD169.fasta (229354 nt)
    114. # H3N2_A-Fukushima-OR808-2023_PB2.fasta (2301 nt)
    115. # H3N2_A-Fukushima-OR808-2023_PB1.fasta (2316 nt)
    116. # H3N2_A-Fukushima-OR808-2023_PA.fasta (2208 nt)
    117. # H3N2_A-Fukushima-OR808-2023_HA.fasta (1722 nt)
    118. # H3N2_A-Fukushima-OR808-2023_NP.fasta (1536 nt)
    119. # H3N2_A-Fukushima-OR808-2023_NA.fasta (1440 nt)
    120. # H3N2_A-Fukushima-OR808-2023_M.fasta (1002 nt)
    121. # H3N2_A-Fukushima-OR808-2023_NS.fasta (865 nt)
    122. # Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta (197140 nt)
    123. # HIV-1_isolate_01IC-PCI127.fasta (9752 nt)

  3. (Optional) Run the first round of vrap (--virus==viruses_selected.fasta)

    1. ln -s ~/Tools/vrap/ .
    2. mamba activate /home/jhuang/miniconda3/envs/vrap
    4. cd ~/DATA/Data_Damian/vrap_Ringversuch
    5. cat complete_10244_ncbi.fasta complete_10298_ncbi.fasta complete_10310_ncbi.fasta complete_1323429_ncbi.fasta complete_10360_ncbi.fasta complete_41857_ncbi.fasta complete_10244_ncbi.fasta complete_11676_ncbi.fasta > viruses_selected.fasta
    7. #Run vrap (first round): replace --virus to the specific taxonomy (e.g. viruses_selected.fasta) --> change virus_user_db --> specific_bacteria_user_db
    8. (vrap) for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
    9.     vrap/vrap.py  -1 ${sample}_R1.fastq.gz -2 ${sample}_R2.fastq.gz  -o vrap_${sample} --bt2idx=/home/jhuang/REFs/genome --host=/home/jhuang/REFs/genome.fa --virus=/home/jhuang/DATA/Data_Damian/vrap_Ringversuch/viruses_selected.fasta --nt=/mnt/nvme1n1p1/blast/nt --nr=/mnt/nvme1n1p1/blast/nr  -t 100 -l 200  -g
    10. done

  4. Run the second round of vrap (--host==${virus}.fasta)

    1. cat Enterovirus_D68_isolate_SH2024-25870.fasta HSV-1_isolate_MacIntyre.fasta HSV-2_strain_G.fasta H1N1_A-PR-8-34_PB2.fasta H1N1_A-PR-8-34_PB1.fasta H1N1_A-PR-8-34_PA.fasta H1N1_A-PR-8-34_HA.fasta H1N1_A-PR-8-34_NP.fasta H1N1_A-PR-8-34_NA.fasta H1N1_A-PR-8-34_M.fasta H1N1_A-PR-8-34_NS.fasta Human_cytomegalovirus_strain_AD169.fasta H3N2_A-Fukushima-OR808-2023_PB2.fasta H3N2_A-Fukushima-OR808-2023_PB1.fasta H3N2_A-Fukushima-OR808-2023_PA.fasta H3N2_A-Fukushima-OR808-2023_HA.fasta H3N2_A-Fukushima-OR808-2023_NP.fasta H3N2_A-Fukushima-OR808-2023_NA.fasta H3N2_A-Fukushima-OR808-2023_M.fasta H3N2_A-Fukushima-OR808-2023_NS.fasta Monkeypox_isolate_MPXV-Germany-2022-RKI513.fasta HIV-1_isolate_01IC-PCI127.fasta > viruses_representative.fasta
    3. # Run vrap (second round): selecte some representative viruses from the generated Excel-files generated by the last step as --host
    4. (vrap) for virus in Enterovirus_D68_isolate_SH2024-25870 HSV-1_isolate_MacIntyre HSV-2_strain_G H1N1_A-PR-8-34_PB2 H1N1_A-PR-8-34_PB1 H1N1_A-PR-8-34_PA H1N1_A-PR-8-34_HA H1N1_A-PR-8-34_NP H1N1_A-PR-8-34_NA H1N1_A-PR-8-34_M H1N1_A-PR-8-34_NS Human_cytomegalovirus_strain_AD169 H3N2_A-Fukushima-OR808-2023_PB2 H3N2_A-Fukushima-OR808-2023_PB1 H3N2_A-Fukushima-OR808-2023_PA H3N2_A-Fukushima-OR808-2023_HA H3N2_A-Fukushima-OR808-2023_NP H3N2_A-Fukushima-OR808-2023_NA H3N2_A-Fukushima-OR808-2023_M H3N2_A-Fukushima-OR808-2023_NS Monkeypox_isolate_MPXV-Germany-2022-RKI513 HIV-1_isolate_01IC-PCI127; do
    5.     for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
    6.         vrap/vrap_until_bowtie2.py  -1 ${sample}_R1.fastq.gz -2 ${sample}_R2.fastq.gz  -o vrap_${sample}_on_${virus} --host /home/jhuang/DATA/Data_Damian/vrap_Ringversuch/${virus}.fasta   -t 100 -l 200  --gbt2 --noblast
    7.     done
    8. done

  5. Generate the mapping statistics for the sam-files generated from last step

    1. #Enterovirus_D68_isolate_SH2024-25870
    2. #for virus in HSV-1_isolate_MacIntyre HSV-2_strain_G H1N1_A-PR-8-34_PB2 H1N1_A-PR-8-34_PB1 H1N1_A-PR-8-34_PA H1N1_A-PR-8-34_HA H1N1_A-PR-8-34_NP H1N1_A-PR-8-34_NA H1N1_A-PR-8-34_M H1N1_A-PR-8-34_NS Human_cytomegalovirus_strain_AD169; do
    3. for virus in H3N2_A-Fukushima-OR808-2023_PB2 H3N2_A-Fukushima-OR808-2023_PB1 H3N2_A-Fukushima-OR808-2023_PA H3N2_A-Fukushima-OR808-2023_HA H3N2_A-Fukushima-OR808-2023_NP H3N2_A-Fukushima-OR808-2023_NA H3N2_A-Fukushima-OR808-2023_M H3N2_A-Fukushima-OR808-2023_NS Monkeypox_isolate_MPXV-Germany-2022-RKI513 HIV-1_isolate_01IC-PCI127; do
    4.     for sample in RV1_DNA RV2_DNA RV3_DNA RV4_DNA RV5_DNA RV6_DNA  RV1_RNA RV2_RNA RV3_RNA RV4_RNA RV5_RNA RV6_RNA; do
    5.         echo "-----${sample}_on_${virus}------" >> LOG_mapping
    6.         cd vrap_${sample}_on_${virus}/bowtie
    7.         # Rename and convert SAM to BAM
    8.         mv mapped mapped.sam 2>> ../../LOG_mapping
    9.         samtools view -S -b mapped.sam > mapped.bam 2>> ../../LOG_mapping
    10.         samtools sort mapped.bam -o mapped_sorted.bam 2>> ../../LOG_mapping
    11.         samtools index mapped_sorted.bam 2>> ../../LOG_mapping
    12.         # Write flagstat output to log (go up two levels to write correctly)
    13.         samtools flagstat mapped_sorted.bam >> ../../LOG_mapping 2>&1
    14.         cd ../..
    15.     done
    16. done
    18. #draw some plots for some representative isolates which found in the first round (see Excel-file).
    19. samtools depth -m 0 -a mapped_sorted.bam > coverage.txt
    20. grep "PQ895337.1" coverage.txt > PQ895337_coverage.txt
    22.         import pandas as pd
    23.         import matplotlib.pyplot as plt
    24.         import sys
    25.         import os
    26.         import re
    28.         # Check for required arguments
    29.         if len(sys.argv) != 3:
    30.             print("Usage: python script.py <coverage_file> <genome_length>")
    31.             sys.exit(1)
    33.         # Parse arguments
    34.         coverage_file = sys.argv[1]
    35.         genome_length = int(sys.argv[2])
    37.         # Extract accession from file name (e.g., "PQ895337" from "PQ895337_coverage.txt")
    38.         file_name = os.path.basename(coverage_file)
    39.         accession_match = re.match(r"([A-Z0-9]+)_coverage\.txt", file_name)
    40.         accession = accession_match.group(1) if accession_match else ""
    42.         # Extract sample name from the grandparent directory of the file
    43.         sample_dir = os.path.basename(os.path.dirname(os.path.dirname(coverage_file)))
    44.         sample_name = re.sub(r'^vrap_', '', sample_dir).replace('_', ' ')
    46.         # Create title and filename
    47.         plot_title = f"{sample_name} ({accession})"
    48.         output_filename = plot_title.replace(" ", "_") + ".png"
    50.         # Load coverage data
    51.         df = pd.read_csv(
    52.             coverage_file,
    53.             sep="\t", header=None, names=["chr", "pos", "coverage"]
    54.         )
    56.         # Create a full genome position index
    57.         full_index = pd.DataFrame({'pos': range(1, genome_length + 1)})
    59.         # Merge coverage data with full index
    60.         df_full = pd.merge(full_index, df[['pos', 'coverage']], on='pos', how='left')
    61.         df_full['coverage'].fillna(0, inplace=True)
    63.         # Plot
    64.         plt.figure(figsize=(10, 4))
    65.         plt.plot(df_full["pos"], df_full["coverage"], color="blue", linewidth=0.5)
    66.         plt.xlabel("Genomic Position")
    67.         plt.ylabel("Coverage Depth")
    68.         plt.title(plot_title)
    69.         plt.tight_layout()
    71.         # Save plot to file
    72.         plt.savefig(output_filename, dpi=150)
    73.         print(f"Plot saved to {output_filename}")
    75.         # Optionally show the plot
    76.         # plt.show()

  6. Report

Subject: Mapping Results and Selected Reference Genomes

Dear XXXX,

Please find below the results of the mapping analysis. For each virus you provided, I have selected a representative reference isolate, listed as follows:

Selected Reference Isolates

  1.     Enterovirus D68
  2.     • PQ895337.1 – Enterovirus D68 isolate SH2024-25870
  4.     HSV-1 (Herpes Simplex Virus 1)
  5.     • PQ569920.1 – Human alphaherpesvirus 1 isolate MacIntyre, complete genome
  7.     HSV-2 (Herpes Simplex Virus 2)
  8.     • OM370995.1 – Human alphaherpesvirus 2 strain G, complete genome
  10.     Influenza A Virus (H1N1)
  11.     • LC662537.1 – PB2 gene, complete CDS
  12.     • LC662538.1 – PB1 and PB1-F2 genes, complete CDS
  13.     • LC662539.1 – PA and PA-X genes, complete CDS
  14.     • LC662540.1 – HA gene, complete CDS
  15.     • LC662541.1 – NP gene, complete CDS
  16.     • LC662542.1 – NA gene, complete CDS
  17.     • LC662543.1 – M1 and M2 genes, complete CDS
  18.     • LC662544.1 – NS1 and NEP genes, complete CDS
  20.     Cytomegalovirus (strain AD169)
  21.     • X17403.1 – Human cytomegalovirus strain AD169, complete genome
  23.     Influenza A Virus (H3N2)
  24.     • LC817404.1 – PB2 gene
  25.     • LC817405.1 – PB1 genes
  26.     • LC817406.1 – PA genes
  27.     • LC817407.1 – HA gene
  28.     • LC817408.1 – NP gene
  29.     • LC817409.1 – NA gene
  30.     • LC817410.1 – M genes
  31.     • LC817411.1 – NS genes
  33.     Monkeypox Virus
  34.     • OP689666.1 – Isolate MPXV/Germany/2022/RKI513, complete genome
  36.     Human Immunodeficiency Virus 1 (HIV-1)
  37.     • AJ866558.1 – Isolate 01IC-PCI127, complete genome

Mapping Results

  1.     We mapped paired-end reads from 12 Ringversuch project samples against the selected reference genomes.
  3.     Below are the mapping statistics for Enterovirus D68, HSV-1, HSV-2, and H1N1. Coverage plots are attached for all cases where the percentage of reads mapping to the reference genome is greater than 0.00%. Results for the remaining viruses will follow next week.
  5.     (* An asterisk indicates cases with non-zero mapping percentages.)

Mapping Statistics

  1.     Enterovirus D68 (SH2024-25870):
  3.     RV1_DNA: 0 (0.00%)
  4.     RV2_DNA: 0 (0.00%)
  5.     RV3_DNA: 0 (0.00%)
  6.     RV4_DNA: 0 (0.00%)
  7.     RV5_DNA: 0 (0.00%)
  8.     RV6_DNA: 0 (0.00%)
  9.     RV1_RNA: 66 (0.00%)
  10.     RV2_RNA: 55 (0.00%)
  11.     RV3_RNA: 15 (0.00%)
  12.     RV4_RNA: 1701 (0.02%) *
  13.     RV5_RNA: 26 (0.00%)
  14.     RV6_RNA: 35 (0.00%)
  16.     HSV-1 (isolate MacIntyre):
  18.     RV1_DNA: 387 (0.02%) *
  19.     RV2_DNA: 6232 (0.26%) *
  20.     RV3_DNA: 0 (0.00%)
  21.     RV4_DNA: 1443 (0.03%) *
  22.     RV5_DNA: 2 (0.00%)
  23.     RV6_DNA: 0 (0.00%)
  24.     RV1_RNA: 6 (0.00%)
  25.     RV2_RNA: 32 (0.00%)
  26.     RV3_RNA: 4 (0.00%)
  27.     RV4_RNA: 13 (0.00%)
  28.     RV5_RNA: 4 (0.00%)
  29.     RV6_RNA: 10 (0.00%)
  31.     HSV-2 (strain G):
  33.     RV1_DNA: 201 (0.01%) *
  34.     RV2_DNA: 376 (0.02%) *
  35.     RV3_DNA: 0 (0.00%)
  36.     RV4_DNA: 19670 (0.46%) *
  37.     RV5_DNA: 0 (0.00%)
  38.     RV6_DNA: 0 (0.00%)
  39.     RV1_RNA: 0 (0.00%)
  40.     RV2_RNA: 3 (0.00%)
  41.     RV3_RNA: 0 (0.00%)
  42.     RV4_RNA: 25 (0.00%)
  43.     RV5_RNA: 5 (0.00%)
  44.     RV6_RNA: 24 (0.00%)
  46.     Influenza A Virus (H1N1, A/PR/8/34):
  48.     RV1_DNA: 0 (0.00%)
  49.     RV2_DNA: 0 (0.00%)
  50.     RV3_DNA: 0 (0.00%)
  51.     RV4_DNA: 0 (0.00%)
  52.     RV5_DNA: 0 (0.00%)
  53.     RV6_DNA: 0 (0.00%)
  54.     RV1_RNA: 0 (0.00%)
  55.     RV2_RNA: 0 (0.00%)
  56.     RV3_RNA: 0 (0.00%)
  57.     RV4_RNA: 13 + 354 (0.00%)
  58.     RV5_RNA: 0 (0.00%)
  59.     RV6_RNA: 0 (0.00%)

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