EPI2ME Labs 23.04-01 Release

We are pleased to release a collection of updates and technical improvements to the EPI2ME Labs bioinformatics workflows.

• wf-single-cell (v0.2.2) is our workflow for the analysis of single-cell transcriptome data. 
  • A more stringent filtering of isoforms is now applied - this uses an approach similar to that performed by the FLAMES software. The change will reduce the number of reads incorrectly assigned to transcripts and thus decrease the number of false positive transcript assignments. 
  • The colours used by the UMAP and gene saturation plots have been updated.
  • Gene IDs were erroneously reported (instead of gene names) in the previous release. This update fixes this issue and gene names are again reported in the result files.
  • Fixed incorrect stripping of barcode insertion characters.
  • Fixed a workflow error when processing contigs that contain no sequence alignments following transcriptome mapping.
• wf-pore-c (v0.0.3) is our workflow for the analysis of sequence data from chromosome conformation capture experiments. 
  • The workflow is considerably faster - input BAM files are now indexed instead of split during the analysis.
  • The workflow now accepts both FASTQ and BAM sequences as input.
  • An HTML report is now produced.
• wf-metagenomics (v2.1.0) provides a workflow for the analysis of metagenomic data. This update includes: 
  • More options to input data: a single file, a directory containing fastq files, or a directory of directories containing fastq files.
  • The HTML report has been updated to use our ezCharts library with new features like:
    • an export button to download tables from the report
    • a stacked barplot which shows the most abundant taxa
    • information of all the taxonomic ranks
  • The workflow now uses the latest version of kraken2-server and has a new option:
    • threads_server for setting --thread-pool on the server
  • Fixes a workflow error when --batch-size=1.
• wf-flu (v0.0.7) provides a workflow for the analysis of influenza genomes.
  • The included INSaFLU database has been updated to v10 – this is used for annotation.
  • The HTML report has been updated to use our ezCharts library and has a new feature: 
    • inclusion of abricate/INSaFLU results for cases where mixed results are discovered
  • The workflow now performs a Nextclade assessment for certain influenza strains.
  • The medaka models for kit14 have been included; sequencing runs with the latest flowcells and sequencing reagents are now supported.
• kraken2-server (v0.1.3) provides a server-client architecture for the kraken2 software. This update addresses an idiosyncratic issue and allows the streaming of input FASTQ through STDIN.