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Contact: Mike Lin (mlin@dnanexus.com) | DNAnexus support (support@dnanexus.com)
DNAnexus and the Sabeti lab have collaborated to provide a cloud-based version of the broadinstitute/viral-ngs pipelines for assembly of viral genomes from metagenomic RNA-seq data; and metagenomic analyses.
To begin using the pipeline, you'll first create a DNAnexus account and project. Then you'll securely upload your NGS data and a couple required software packages. The pipeline can take several hours to run, depending on the experimental design and sequencing depth.
An essential component of the pipeline involves depleting the input dataset of any reads matching the human genome/transcriptome, so that the remaining "cleaned" metagenomic data may be shared or published with reduced privacy risks.
More specific information about the assembly workflow and metagenomics workflow can be found at their respective wiki pages.
If your samples are multiplexed to sequencing lanes, the data should be demultiplexed prior to upload. Please refer to the wiki page on Demultiplexing and BCL to reads conversion for instructions on this procedure.