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

<p><strong>Context</strong></p> <p>These files correspond to the article&nbsp;&ldquo;Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery&rdquo; submitted to Genes.</p> <p>&nbsp;</p> <p><strong>File content</strong></p> <ul> <li>input_data-empty_matrices:&nbsp;50M-read Tissues and Plasma matrices, no spike;</li> <li>input_data-matrices_spiked_known_viruses:&nbsp;50M-read Tissues and Plasma matrices spiked with six known virus at d1, d10, d100;</li> <li>input_data-matrices_spiked_neo_viruses:&nbsp;50M-read Tissues and Plasma matrices spiked with 3 Neopneumoviruses at d1 and d10;</li> <li>input_data-neo_viruses:&nbsp;Nucleotide and protein sequences of 3 Neopeumoviruses</li> <li>input_data-tick_sample:&nbsp;raw data of a Rhipicephalus tick sample known to be infected with the Cataloi Tick Quaranjavirus (CTQV)</li> <li>input_data-negative_control:&nbsp;raw data of the negative control (water)</li> <li>output_microseek:&nbsp;Microseek outputs, raw results and results after background filtration</li> </ul> <p>&nbsp;</p> <p><strong>File listing&nbsp;</strong></p> <pre><code class="language-bash">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 </code></pre> <p>&nbsp;</p>