Tools and Databases
ViromeXplore uses the following versions of the bioinformatics tools:
Software |
Version |
Summary |
Links |
|---|---|---|---|
VirSorter2 |
2.2.3 |
Identifies and classifies viral sequences from metagenomic assemblies. |
|
CheckV |
0.8.1 |
Quality assessment of viral genomes. |
|
CD-HIT |
4.8.1 |
Clustering tool for reducing sequence redundancy. |
|
ViromeQC |
1.0.2 |
Benchmark and quantify non-viral contamination. |
|
Kaiju |
1.7.2 |
Taxonomic classification of metagenomic reads. |
|
Krona |
2.8 |
Interactive hierarchical visualization of metagenomic data. |
|
FlashWeave |
0.19.2 |
Infers microbial interaction networks from sequencing data. |
|
TIM |
latest |
Interactions between organisms through phylogeny and co-occurence. |
|
fastp |
0.20.1 |
FASTQ preprocessing tool (quality filtering, trimming). |
|
MEGAHIT |
1.2.9 |
Ultrafast assembler for large and complex metagenomes. |
|
Bowtie2 |
2.4.1 |
Fast and sensitive short-read alignment. |
|
SAMtools |
1.9 |
Utilities for manipulating alignments in SAM/BAM formats. |
|
MetaBAT2 |
2.15 |
Genome binning from metagenomic assemblies. |
|
COBRA |
1.2.3 |
Higher quality viral genomes assembled from metagenomes. |
|
geNomad |
1.8.0 |
Virus identification, classification and annotation tool. |
|
EggNOG-mapper |
2.1.9 |
Functional annotation using orthology assignments. |
|
VSEARCH |
2.10.4 |
Open-source tool for metagenomic clustering, chimera detection, and search. |
ViromeXplore uses the following reference databases.
Database |
Version |
Summary |
Links |
|---|---|---|---|
CheckV database |
v1.0 |
Database for viral genome quality assessment with CheckV. |
|
EggNOG database |
v5.0.2 |
Orthology-based functional annotation database used by EggNOG-mapper. |
|
geNomad database |
v1.7 |
Reference database for viral discovery and annotation with geNomad. |
|
Kaiju virus database |
2024-08-15 |
Taxonomic classification database for viral sequences in Kaiju. |
|
Virus-Host Database |
latest |
Reference database of known virus-host interactions. |
Note
Consider citing the tools and databases used in ViromeXplore accordingly.