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peterk87 / nf-villumina

Generic viral Illumina sequence analysis pipeline
MIT License
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Add metaviralSPAdes assembly #18

Open peterk87 opened 4 years ago

peterk87 commented 4 years ago

metaviralSPAdes: assembly of viruses from metagenomic data

MOTIVATION: Although the set of currently known viruses has been steadily expanding, only a tiny fraction of the Earth's virome has been sequenced so far. Shotgun metagenomic sequencing provides an opportunity to reveal novel viruses but faces the computational challenge of identifying viral genomes that are often difficult to detect in metagenomic assemblies. RESULTS: We describe a metaviralSPAdes tool for identifying viral genomes in metagenomic assembly graphs that is based on analyzing variations in the coverage depth between viruses and bacterial chromosomes. We benchmarked metaviralSPAdes on diverse metagenomic datasets, verified our predictions using a set of virus-specific Hidden Markov Models, and demonstrated that it improves on the state-of-the-art viral identification pipelines. AVAILABILITY: metaviralSPAdes includes viralAssembly, viralVerify, and viralComplete modules that are available as standalone packages: https://github.com/ablab/spades/tree/metaviral_publication, https://github.com/ablab/viralVerify/ and https://github.com/ablab/viralComplete/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

zhaoxvwahaha commented 3 years ago

@peterk87 Hi， Thank you very much for developing the wonderful metaviralSPAdes, is it suitble for RNA virus? If not, what tools can be used to assembly the RNA virus from metatranscriptome, could you give some advice?