This directory includes scripts related to the manuscript "A diverse gut virome from Drosophila melanogaster".
Part1: Preprocessing
Includes metagenomic data preprocessing and assembly: Trimming reads and removing host reads (Drosophila melanogaster), generating high-quality sequences. Then assemble short reads into long contigs.
Part2: Virus discovery
This part includes steps for predicting viral contigs.
Part3: vMAG
The discovered viral contigs were checked for redundancy and virus metagenome-assembled genomes were constructed
Part4:Taxonomy and host assignment
This part includes steps of protein clustering, taxonomy of viral contigs, and host assignment of viral contigs
| Tool | Link |
|---|---|
| TrimGalore | TrimGalore |
| bbmap | bbmap |
| Python scripts | github.com/mehregan59/ |
| megahit | megahit |
| VIBRANT | VIBRANT |
| VirSorter | VirSorter |
| DeepVirFinder | DeepVirFinder |
| vRhyme | vRhyme |
| CheckV | CheckV |
| Cenote-Taker2 | Cenote-Taker2 |
| vpf-tools | vpf-tools |
| diamond | diamond |
| vConTACT2 | vConTACT2 |
| Cytoscape | Cytoscape |
| CrisprOpenDB | CrisprOpenDB |