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EBI_Functional_pipeline
See planet-microbe-functional-annotation repo.
My install notes in my log page, and this issue
Attempt to re-create EBI functional pipeline version 4.1 on cyverse Ubuntu 18_04 NoDesktop Base cloud image.
download from https://sourceforge.net/projects/fraggenescan/files/
get the latest for example wget https://sourceforge.net/projects/fraggenescan/files/FragGeneScan1.31.tar.gz/download
mv download FragGeneScan1.31.tar.gz
tar -zxvf FragGeneScan1.31.tar.gz
make executable:
make fgs
example test: ./run_FragGeneScan.pl -genome=./example/NC_000913-454.fna -out=./example/NC_000913-454-fgs -complete=0 -train=454_10
This will output .faa (protein) or .ffn (nucleotide) fasta files which can be fed into interproscan. Has a flag for the train field which depends on the platform and error rate, would need to extract this info from the fastaQ files (can get error rate) and the metadata in SRA should have the platform type (illumina, sanger 454).
install and run, has optional flag --goterms to switch on corresponding GO terms to Interpro annotations. --applications flag for which analyses and I believe Bonnie said we'd just use PFAM