search

np-core / nanopath

Python package and command line interface - entry point for the repository :snake:
Other
5 stars 0 forks source link

Kraken processing #7

Closed esteinig closed 4 years ago

esteinig commented 4 years ago

Remodel the pipelines.MetagenomePipeline class into a processing class processing.KrakenProcess. Currently implements assessment of artificial mixtures [see #4 ] through processing.KrakenProcess.assess_composition to track classification of known host and microbial reads. Will be used for decontamination of host reads [see #5 ] and then to prepare server data as part of the sepsis Nextflow.

esteinig commented 4 years ago

Explanation of composition assessment to investigate host assignment in https://github.com/np-core/nanopath/issues/5#issuecomment-585586423

esteinig commented 4 years ago

get_server_data in nanopath.processors.KrakenProcessor closed in 1b0212e