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README.md

Binder for BVCN FeGenie lesson

Initially forked from here. Thank you to the awesome binder team!

Binder

Part of the Bioinformatics Virtual Coordination Network :)

Walkthrough

Enter the main FeGenie directory

cd FeGenie

print the FeGenie help menu

FeGenie -h

run FeGenie on test dataset

FeGenie.py -bin_dir genomes/ -bin_ext fna -out fegenie_out

Go into the output directory and check out the output files

cd fegenie_out
less FeGenie-geneSummary-clusters.csv

run FeGenie on gene calls

FeGenie.py -bin_dir ORFs/ -bin_ext faa -out fegenie_out --orfs

run FeGenie on gene calls, and use reference database (RefSeq sub-sample) for cross-validation

FeGenie.py -bin_dir ORFs/ -bin_ext faa -out fegenie_out --orfs -ref refseq_db/refseq_nr.sample.faa

About

Two introductory lectures and tutorial on the microbial iron cycle and FeGenie

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