Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery"

Context

These files correspond to the article “Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery” submitted to Genes.

File content

• input_data-empty_matrices: 50M-read Tissues and Plasma matrices, no spike;
• input_data-matrices_spiked_known_viruses: 50M-read Tissues and Plasma matrices spiked with six known virus at d1, d10, d100;
• input_data-matrices_spiked_neo_viruses: 50M-read Tissues and Plasma matrices spiked with 3 Neopneumoviruses at d1 and d10;
• input_data-neo_viruses: Nucleotide and protein sequences of 3 Neopeumoviruses
• input_data-tick_sample: raw data of a Rhipicephalus tick sample known to be infected with the Cataloi Tick Quaranjavirus (CTQV)
• input_data-negative_control: raw data of the negative control (water)
• output_microseek: Microseek outputs, raw results and results after background filtration

File listing 

input_data-empty_matrices.tar.xz
├── plasma.fastq 
└── tissue.fastq 

input_data-matrices_spiked_known_viruses
├── d1 
│   ├── spiked_plasma.fastq
│   └── spiked_tissue.fastq
├── d10 
│   ├── spiked_plasma.fastq
│   └── spiked_tissue.fastq
└── d100 
    ├── spiked_plasma.fastq
    └── spiked_tissue.fastq

input_data-matrices_spiked_neo_viruses.tar.xz
├── d1 
│   ├── plasma_spiked_with_neo1.fastq
│   ├── plasma_spiked_with_neo2.fastq
│   ├── plasma_spiked_with_neo3.fastq
│   ├── tissue_spiked_with_neo1.fastq
│   ├── tissue_spiked_with_neo2.fastq
│   └── tissue_spiked_with_neo3.fastq
└── d10 
    ├── plasma_spiked_with_neo1.fastq
    ├── plasma_spiked_with_neo2.fastq
    ├── plasma_spiked_with_neo3.fastq
    ├── tissue_spiked_with_neo1.fastq
    ├── tissue_spiked_with_neo2.fastq
    └── tissue_spiked_with_neo3.fastq

input_data-neo_viruses.tar.xz
├── genes 
│   ├── neo_1.fasta
│   ├── neo_2.fasta
│   └── neo_3.fasta
└── proteins 
    ├── neo_1.fasta
    ├── neo_2.fasta
    └── neo_3.fasta

input_data-tick_sample.tar.xz
└── Cataloi_S1_R1_001.fastq.xz

input_data-negative_control.tar.xz
└── negative_control.fastq.xz


output_microseek.tar.xz
├── empty_matrices
│   ├── matrix_plasma
│   └── matrix_tissue
├── matrices_spiked_known_viruses
│   ├── filtered
│   │   ├── d100_plasma
│   │   ├── d100_tissue
│   │   ├── d10_plasma
│   │   ├── d10_tissue
│   │   ├── d1_plasma
│   │   └── d1_tissue
│   └── non_filtered
│       ├── d100_plasma
│       ├── d100_tissue
│       ├── d10_plasma
│       ├── d10_tissue
│       ├── d1_plasma
│       └── d1_tissue
├── matrices_spiked_neo_viruses
│   ├── filtered
│   │   ├── plasma_spiked_with_neo1_at_d1
│   │   ├── plasma_spiked_with_neo1_at_d10
│   │   ├── plasma_spiked_with_neo2_at_d1
│   │   ├── plasma_spiked_with_neo2_at_d10
│   │   ├── plasma_spiked_with_neo3_at_d1
│   │   ├── plasma_spiked_with_neo3_at_d10
│   │   ├── tissue_spiked_with_neo1_at_d1
│   │   ├── tissue_spiked_with_neo1_at_d10
│   │   ├── tissue_spiked_with_neo2_at_d1
│   │   ├── tissue_spiked_with_neo2_at_d10
│   │   ├── tissue_spiked_with_neo3_at_d1
│   │   └── tissue_spiked_with_neo3_at_d10
│   └── non_filtered
│       ├── plasma_spiked_with_neo1_at_d1
│       ├── plasma_spiked_with_neo1_at_d10
│       ├── plasma_spiked_with_neo2_at_d1
│       ├── plasma_spiked_with_neo2_at_d10
│       ├── plasma_spiked_with_neo3_at_d1
│       ├── plasma_spiked_with_neo3_at_d10
│       ├── tissue_spiked_with_neo1_at_d1
│       ├── tissue_spiked_with_neo1_at_d10
│       ├── tissue_spiked_with_neo2_at_d1
│       ├── tissue_spiked_with_neo2_at_d10
│       ├── tissue_spiked_with_neo3_at_d1
│       └── tissue_spiked_with_neo3_at_d10
├── negative_control
└── tick_sample