ONT Pipeline - Githubissues

EBI-Metagenomics / ebi-metagenomics-cwl

This repository contains the CWL description of the EBI Metagenomics pipeline

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Open rdfinn opened 7 years ago

rdfinn commented 7 years ago

We need to start thinking about how we should run ONT data

[x] QC using poretools
[x] Functional assignments using nhmmer and pfam
[ ] The functional assignments looks really good, need a Pfam2GO, or Pfam -> InterPro2GO
[ ] Kmer based taxonomy profiling
[ ] Standard SSU/LSU approach, may need to take top hit? Does mapseq do any thing different.

rdfinn commented 7 years ago

poretools fasta <path to directory containing the ‘pass’ fast5 files> >