This week the EPI2ME Labs team is delighted to release a new workflow,
wf-bacterial-genomes. We have also released minor updates to wf-artic,
wf-alignment and wf-isoforms.
wf-bacterial-genomes is a Nextflow workflow implemented to simplify bacterial
genome assembly. The analysis pipeline performs a quality review on the starting
sequence collection prior to assembling the provided sequencing data using Flye.
The consensus sequence is polished using Medaka and some basic annotation is
performed using Prokka. If a reference genome is provided, the workflow will map
sequence reads to this reference using minimap2 and will call variants using
medaka variant. This workflow replaces our earlier wf-hap-snp product that
performed variant calling in haploid genomes.
wf-artic for the analysis of
SARS-CoV-2 sequencing data has been updated to version v0.3.12. This release
includes an update to the included version of Nextclade (1.10.3) and
improvements to the Nextclade visualisation included in the HTML report. Please
note that the workflow now uses the r941_min_hac_variant_g507 Medaka model by
default. The corresponding EPI2ME workflow, Fastq QC + ARTIC + NextClade, also
includes these updates and is available as version v2022.03.08. Please see the
product changelog for additional details.
wf-alignment, our workflow for mapping sequence reads to a reference genome, has
been updated to version v0.1.1. This minor update introduces a collection of
performance changes - for more details please review the workflow changelog.
wf-isoforms, for analysis of gene isoforms from cDNA sequencing data, has been
updated to version v0.1.1. This update fixes a couple of issues associated with
transcript counting and the de novo approach to identifying genes and their
isoforms. More information on these updates is provided in the product’s
Our metagenomic classification tutorial has been fixed. The bundled
Centrifuge software can now find the required indices.
We would welcome any recommendations for future workflows, tutorials and dataset