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results/
├── 00_quality_filtering
│ └── sample_name
│ │ ├── sample_name_18-25nt_cutadapt.log
│ │ ├── sample_name_fastqc.html
│ │ ├── sample_name_fastqc.zip
│ │ ├── sample_name_21-22nt_cutadapt.log
│ │ ├── sample_name_21-22nt.fastq.gz
│ │ ├── sample_name_24nt_cutadapt.log
│ │ ├── sample_name_blacklist_filter.log
│ │ ├── sample_name_fastp.html
│ │ ├── sample_name_fastp.json
│ │ ├── sample_name_qual_filtering_cutadapt.log
│ │ ├── sample_name_quality_trimmed_fastqc.html
│ │ ├── sample_name_quality_trimmed_fastqc.zip
│ │ ├── sample_name_quality_trimmed.fastq.gz
│ │ ├── sample_name_read_length_dist.pdf
│ │ ├── sample_name_read_length_dist.txt
│ │ ├── sample_name_truseq_adapter_cutadapt.log
│ │ └── sample_name_umi_tools.log
│ └── qc_report
│ ├── read_origin_counts.txt
│ ├── read_origin_detailed_pc.txt
│ ├── read_origin_pc_summary.txt
│ ├── read_origin_pc_summary.txt
│ ├── run_qc_report.txt
│ └── run_read_size_distribution.pdf
├── 01_VirReport
│ └── sample_name
│ │ └── alignments
│ │ │ └──NT
│ │ │ │ ├── sample_name_21-22nt_all_targets_with_scores.txt
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_bowtie_log.txt
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.consensus.fasta
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.dedup.bam
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.dedup.bam.bai
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.fa
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.fa.fai
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_norm.bcf
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_norm.bcf.csi
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_norm_flt_indels.bcf
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_norm_flt_indels.bcf.csi
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_picard_metrics.txt
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_sequence_variants.vcf.gz
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_sequence_variants.vcf.gz.csi
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_umi_tools.log
│ │ │ │ ├── sample_name_21-22nt_top_scoring_targets.txt
│ │ │ │ └── sample_name_21-22nt_top_scoring_targets_with_cov_stats.txt
│ │ │ └──viral_db
│ │ │ │ ├── sample_name_21-22nt_all_targets_with_scores.txt
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_bowtie_log.txt
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.consensus.fasta
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.dedup.bam
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.dedup.bam.bai
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.fa
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name.fa.fai
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_norm.bcf
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_norm.bcf.csi
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_norm_flt_indels.bcf
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_norm_flt_indels.bcf.csi
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_picard_metrics.txt
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_sequence_variants.vcf.gz
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_sequence_variants.vcf.gz.csi
│ │ │ │ ├── sample_name_21-22nt_GenBankID_virus_name_umi_tools.log
│ │ │ │ └── sample_name_21-22nt_top_scoring_targets_with_cov_stats_viraldb.txt
│ │ └── assembly
│ │ │ ├── sample_name_cap3_21-22nt.fasta
│ │ │ ├── sample_name_spades_assembly_21-22nt.fasta
│ │ │ ├── sample_name_spades_log
│ │ │ ├── sample_name_velvet_assembly_21-22nt.fasta
│ │ │ └── sample_name_velvet_log
│ │ └──blastn
│ │ │ └── NT
│ │ │ │ ├── sample_name_cap3_21-22nt_blastn_vs_NT.bls
│ │ │ │ ├── sample_name_cap3_21-22nt_blastn_vs_NT_top5Hits.txt
│ │ │ │ ├── sample_name_cap3_21-22nt_blastn_vs_NT_top5Hits_virus_viroids_final.txt
│ │ │ │ ├── sample_name_cap3_21-22nt_blastn_vs_NT_top5Hits_virus_viroids_seq_ids_taxonomy.txt
│ │ │ │ └── summary_sample_name_cap3_21-22nt_blastn_vs_NT_top5Hits_virus_viroids_final.txt
│ │ │ └── viral_db
│ │ │ ├── sample_name_cap3_21-22nt_blastn_vs_viral_db.bls
│ │ │ ├── sample_name_cap3_21-22nt_megablast_vs_viral_db.bls
│ │ │ ├── summary_sample_name_cap3_21-22nt_blastn_vs_viral_db.bls_filtered.txt
│ │ │ ├── summary_sample_name_cap3_21-22nt_blastn_vs_viral_db.bls_viruses_viroids_ICTV.txt
│ │ │ ├── summary_sample_name_cap3_21-22nt_megablast_vs_viral_db.bls_filtered.txt
│ │ │ └── summary_sample_name_cap3_21-22nt_megablast_vs_viral_db.bls_viruses_viroids_ICTV.txt
│ │ ├── blastx
│ │ │ └── NT
│ │ │ ├── sample_name_cap3_21-22nt_blastx_vs_NT.bls
│ │ │ ├── sample_name_cap3_21-22nt_blastx_vs_NT_top5Hits.txt
│ │ │ ├── sample_name_cap3_21-22nt_blastx_vs_NT_top5Hits_virus_viroids_final.txt
│ │ │ └── summary_sample_name_cap3_21-22nt_blastx_vs_NT_top5Hits_virus_viroids_final.txt
│ │ └── tblastn
│ │ └── viral_db
│ │ ├── sample_name_cap3_21-22nt_getorf.all.fasta
│ │ ├── sample_name_cap3_21-22nt_getorf.all_tblastn_vs_viral_db_out.bls
│ │ └── sample_name_cap3_21-22nt_getorf.all_tblastn_vs_viral_db_top5Hits_virus_viroids_final.txt
│ └── Summary
│ ├── run_top_scoring_targets_with_cov_stats_with_cont_flag_FPKM_0.01_21-22nt.txt
│ └── run_top_scoring_targets_with_cov_stats_with_cont_flag_FPKM_0.01_21-22nt_viral_db.txt
└── 02_VirusDetect
└── sample_name
│ ├── blastn.reference.fa
│ ├── blastn_references
│ ├── blastx.reference.fa
│ ├── blastx_references
│ ├── contig_sequences.blastn.fa
│ ├── contig_sequences.blastx.fa
│ ├── contig_sequences.fa
│ ├── contig_sequences.undetermined.fa
│ ├── sample_name_21-22nt.blastn.html
│ ├── sample_name_21-22nt.blastn.sam
│ ├── sample_name_21-22nt.blastn_spp.txt
│ ├── sample_name_21-22nt.blastn.summary.filtered.txt
│ ├── sample_name_21-22nt.blastn.summary.txt
│ ├── sample_name_21-22nt.blastn.txt
│ ├── sample_name_21-22nt.blastx.html
│ ├── sample_name_21-22nt.blastx.sam
│ ├── sample_name_21-22nt.blastx.summary.txt
│ └── sample_name_21-22nt.blastx.txt
└── Summary
├── run_summary_top_scoring_targets_virusdetect_21-22nt_filtered.txt
└── run_summary_virusdetect_21-22nt.txt |
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Under the 00_quality_filtering folder:
◦ a folder is created for each sample which contains zipped quality filtered fastq files, associated QC files and logs
◦ under the QC_report folder, read size distribution pdf file and read RNA source pdf file are created. The folder also includes a run_qc_report text file
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Under the 01_VirReport folder:
For each sample:
assembly: results associated with de novo assembly
blastn: megablast results (NCBI NT or viral database PVirDB)
blastx: blastx results against NR
tblastn: tblastn results against viral database PVirDB
alignments: alignment against top reference hit and associated statistic derivation
Summary
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