[Question] Using Struo for taxonomic assingment with MetaPhlAn3

[TakacsBertalan]

Hi! I don't know if this repository is still maintained, but Struo almost looks like the solution for my problem, so I will just try. I would like to create a custom reference for MetaPhlAn3. I am only interested in taxonomical profiling. Is it possible to use the database created with Struo as a MetaPhlAn3 database, either during running Humann3 or separately?
In your tutorial, I can see that the default metaphlan databases are used, but the use of "skip" is not very clear to me in this instance.

STRUO_OUT_DIR=./struo_output/
NUC_DB=dirname $STRUO_OUT_DIR"/all_genes_annot.fna.gz"
PROT_DB=dirname $STRUO_OUT_DIR"/all_genes_annot.dmnd"
MTPHLN_BT2_DB=dirname ./metaphlan2_db/mpa_v20_m200/mpa_v20_m200.1.bt2
MTPHLN_PKL_DB=/ebio/abt3_projects2/databases_no-backup/metaphlan2/mpa_v20_m200/mpa_v20_m200.pkl

humann2 --gap-fill on --bypass-nucleotide-index
--nucleotide-database $NUC_DB
--protein-database $PROT_DB
--metaphlan-options "Skip --mpa_pkl $MTPHLN_PKL_DB --bowtie2db $MTPHLN_BT2_DB"
--tmp-dir /dev/shm/humann2_temp/
--threads 12
--input-format fastq
--output-basename SRS018656
--input SRS018656_R1.fq

Does this mean that the command completely skips the metaphlan taxonomic assignment and just does the functional analysis with humann?

Thanks in advance!

[nick-youngblut]

Hi! I don't know if this repository is still maintained, but Struo almost looks like the solution for my problem

@TakacsBertalan I highly recommend using Struo2 instead of Struo