jd-x1 / compact_classification

compact_class

Instructions

compact_class is designed to classify newly generated MAGs using multiple single gene phylogenetic placement.

Be Aware of MAG naming conventions

Step 0: Download PhyloFisherDB

cd resources
wget https://ndownloader.figshare.com/files/29093409
tar -xzvf 29093409
rm 29093409
cd ..

Step 1: Ensure MAGS end in extension '.fna'

Current behavior is implemented to allow me to control which files in a folder I want to be put through the pipeline without having to delete/move files.

[MAGname].fna # different fasta file extensions will not be detected 

Also avoid the following symbols in the name as certain tools in this pipeline do not interact well with them.

'_'
'@'
'..'
'whitespace'
'*'

Step 2: Run pipeline

Be aware no clean up options have been implemented quite yet. As a result this will produce quite a few intermediary directories and steps in the resources directory.

sh comp_class.sh -m [directory containing MAGs]