DOI: 10.5281/zenodo.6937000
title: Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery"

description: <strong>Context</strong> These files correspond to the article “Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery” submitted to Genes. <strong>File content</strong> 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 <strong>File listing </strong> <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>