EPI2ME Labs 23.02-01 Release

By Stephen Rudd
Published in Software Releases
February 08, 2023
1 min read
EPI2ME Labs 23.02-01 Release

Dear Nanopore Community,

This release Wednesday we are pleased to include CNV detection in our human variation workflow, wf-human-variation. We introduce a new addition to the Oxford Nanopore Open Data project - the Genome In a Bottle Ashkenazi trio. Other functional and performance improvements are also described.

  • A final version v0.0.9 (CHANGELOG) of wf-cnv has been made. This includes a collection of memory usage improvements and a malformed VCF fix. This product has also been wrapped into the wf-human-variation workflow. The wf-cnv product is therefore deprecated and users should instead use wf-human-variation, which will receive ongoing updates and improvements.
  • wf-human-variation has been updated to release v1.2.0 (CHANGELOG). The workflow now includes the functionality from wf-cnv, (see above). This provides functionality for the identification of copy number variation in addition to SNV, SV, and base-modification changes.
  • wf-single-cell is now available with release v0.2.0 (CHANGELOG). This update includes a minor improvements to UMI identification and a fix for an issue that resulted in too few transcripts being identified.
  • wf-bacterial-genomes has been updated to release v0.2.11 (CHANGELOG). This update includes a simplification for users to make it easier to ensure the correct consensus or variant parameters are chosen for use with medaka.
  • wf-clone-validation has been updated to release v0.2.8 (CHANGELOG) and includes the same medaka improvements noted for wf-bacterial-genomes above.
  • modbam2bed has been updated to release v0.8.0 (CHANGELOG). This version adds a --combine option to combine calls from all modified bases in a family. The previous behaviour was that the non-modified (canonical) count would be incremented. For example when searching for 5mC modifications with -m 5mC and a 5hmC base was present, the read would contribute to the canonical count, not the modified count. See the README for more information.
  • A new dataset in the Oxford Nanopore Open Data project has been released. DNA sequencing data from the Genome in a Bottle Ashkenazi trio has been prepared using Ligation Sequencing Kit V14. FAST5 signal data is included for genomes HG002, HG003, and HG004. The wf-human-variation workflow has been run  for each of these three genomes using both HAC and SUP basecalling models. Please see the data release post for more information on the samples and for information on how the Amazon Web Services S3 bucket may be accessed.

We would be delighted to receive any feedback and welcome recommendations for future workflow or Oxford Nanopore Open Data releases.




Stephen Rudd

Stephen Rudd

Director, Bioinformatics Product

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