Dear Nanopore Community,
With this first June release, we are delighted to update our EPI2ME workflows with some exciting new functionality and a number of other improvements.
--isolatesmode. This introduces some exciting new functionality:
pointfindermethod from Resfinder is run automatically using species information determined by the MLST analysis step described above. This update accommodates isolate samples of unknown species, or runs where you have multiple barcoded isolates, and will provide a full AMR analysis.
--snpanalysis will now produce VCF format output files that now also contain functional annotations from SnpEff. The HTML report now includes a table of variants annotated using the ClinVar resource.
chunk_sizeparameter has been updated to a default value of
25000- this will address some memory usage issues.
We would welcome recommendations for new workflows that would benefit your research and would love to hear about new functionality to our existing workflows.