1. Description of the methods¶
1.1. Taxonomic read filtration¶
1.1.1. Human, contaminant, and duplicate read removal¶
The assembly pipeline begins by depleting paired-end reads from each sample of human and other contaminants using BMTAGGER and BLASTN, and removing PCR duplicates using M-Vicuna (a custom version of Vicuna).
1.3. Taxonomic read identification¶
Nothing here at the moment. That comes later, but we will later integrate it when it’s ready.
1.4. Cloud compute implementation¶
This assembly pipeline is also available via the DNAnexus cloud platform. RNA paired-end reads from either HiSeq or MiSeq instruments can be securely uploaded in FASTQ or BAM format and processed through the pipeline using graphical and command-line interfaces. Instructions for the cloud analysis pipeline are available at https://github.com/dnanexus/viral-ngs/wiki