| _version_ | 1866902113545617408 |
|---|---|
| author | Patricia |
| author_facet | Patricia |
| contents | <p><strong>EVEREST</strong> (pip<strong>E</strong>line for <strong>V</strong>iral ass<strong>E</strong>mbly and cha<strong>R</strong>act<strong>E</strong>ri<strong>S</strong>a<strong>T</strong>ion) is a comprehensive, end-to-end pipeline designed for virus discovery and characterization. Implemented in Nextflow, it processes Illumina single- and paired-end reads through five key phases: pre-processing, filtering, de novo assembly, refinement, and classification. The pipeline ensures high-quality data by trimming, removing host sequences, eliminating duplicates, and applying digital normalization. It then assembles viral genomes using a de novo assembly strategy, clusters similar contigs, captures viral genomes, and assesses their quality. Finally, <strong>EVEREST</strong> classifies viral contigs using the NCBI (nucleotide) and Uniprot (amino acid) databases, providing a robust framework for identifying and characterizing viruses from sequencing data.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_14963685 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | A Nextflow-Based Automated Pipeline for Viral Assembly and Characterisation (EVEREST) Patricia <p><strong>EVEREST</strong> (pip<strong>E</strong>line for <strong>V</strong>iral ass<strong>E</strong>mbly and cha<strong>R</strong>act<strong>E</strong>ri<strong>S</strong>a<strong>T</strong>ion) is a comprehensive, end-to-end pipeline designed for virus discovery and characterization. Implemented in Nextflow, it processes Illumina single- and paired-end reads through five key phases: pre-processing, filtering, de novo assembly, refinement, and classification. The pipeline ensures high-quality data by trimming, removing host sequences, eliminating duplicates, and applying digital normalization. It then assembles viral genomes using a de novo assembly strategy, clusters similar contigs, captures viral genomes, and assesses their quality. Finally, <strong>EVEREST</strong> classifies viral contigs using the NCBI (nucleotide) and Uniprot (amino acid) databases, providing a robust framework for identifying and characterizing viruses from sequencing data.</p> |
| title | A Nextflow-Based Automated Pipeline for Viral Assembly and Characterisation (EVEREST) |
| url | https://doi.org/10.5281/zenodo.14963685 |