Nanopore reads, input convert it to FASTQ format

[dgoswamia]

Hello,
It does say in the description that this is for PacBio long-read sequencing processing. I like the output format of laava. I am wondering if I can use the Nanopore FASTQ file as a input and will get the analysis pipeline as a pacbio sample. What is the caveat I need to think about while processing the Nanopore FASTQ read file using the laava pipeline?

{
  "seq_reads_file": "test/samples/nanopore.fastq",
  "vector_type": "sc",
  "vector_bed": "test/samples/sc.annotation.bed",
  "vector_fa": "test/samples/sc.construct.fasta",
  "packaging_fa": "test/fasta/packaging.fa",
  "host_fa": "test/fasta/hg38.chr19trunc-chrM.fa",
  "itr_label_1": "ITR-L",
  "itr_label_2": "ITR-R",
  "repcap_name": "pRep2Cap9",
  "helper_name": "pHelper",
  "lambda_name": "Lambda",
  "target_gap_threshold": 200,
  "max_allowed_outside_vector": 100,
  "max_allowed_missing_flanking": 100,
  "container_version": ":dev"
}

Thanks

[etal]

It should work as-is, actually. We just haven't validated it on nanopore samples or tuned it for that platform.

Let me know how it goes, and if there are any problems, I can try to sort them out.

Also note ONT's own, similar pipeline (research-only license): https://github.com/epi2me-labs/wf-aav-qc

[etal]

Also, scAAV might need special preprocessing -- compare to the PacBio approach that is now handled on-instrument with "AAV mode".