Workflows
What is a Workflow?Filters
Assembly of SARS-CoV-2 from pre-processed reads
Live Resources
usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be
What's the point?
Use a combination of Illumina and Oxford Nanopore reads to produce SARS-CoV-2 genome assembly.
Outline
We use Illumina and Oxford Nanopore reads that were pre-processed to remove human-derived sequences. We use two assembly tools: spades and unicycler. While spades is a tool fully dedicated to assembly, unicycler is a "wrapper" that combines multiple existing ...
DownloadPreprocessing of raw SARS-CoV-2 reads
The raw reads available so far are generated from bronchoalveolar lavage fluid (BALF) and are metagenomic in nature: they contain human reads, reads from potential bacterial co-infections as well as true COVID-19 reads.
Live Resources
usegalaxy.org usegalaxy.eu usegalaxy.org.au usegalaxy.be
What's the point?
Assess quality of reads, remove adapters and remove reads mapping to human genome.
The outline
Illumina and Oxford nanopore reads are pulled from the ...
