Dear Nanopore Community
In this post London Calling ‘24 release we are delighted to introduce a broad collection of updates, improvements, and modifications to our EPI2ME Desktop Application, and the bioinformatics workflows that it can orchestrate. These updates were presented by Sirisha, Sarah, and Natalia during their presentations.
--poly-a-config
(More info here: https://github.com/nanoporetech/dorado?tab=readme-ov-file#polya-tail-estimation)BC
(barcode) tag will be added to the output CRAM
file and demuxed BAM
s will be produced in the folderdemuxed
when you specify --barcode_kit
. Demuxing parameters can be tuned with the addition of any of dorado demux
args with the parameter --demux_args
min_percent_identity
) and the reference covered (min_ref_coverage
) are considered as unclassified in the minimap2 approach.kraken2_memory_mapping
is used.full_reference
parameter for some additional assembly vs provided reference QC and a pLannotate bug fix--bam
) AV:Z
).output_genometype_bams
.--bam
)--plot_umaps
)--merge_bam
)--adapter_scan_chunk_size
and --process_chunk_size
replaced with --fastq_chunk
--kit_name
and --kit_version
replaced with --kit
(eg: --kit 3prime:v3
)Please do let us know your feedback and we’re eager to hear wonderful new ideas for workflows and tutorials. Do watch our blog posts that will further describe some of these updates.
Information