-
Notifications
You must be signed in to change notification settings - Fork 4
1. more info on prepTG
prepTG creates a database directory of genomes to search for homologous instances of reference/query gene-clusters in using fai.
The input is simply a directory of either FASTA or GenBank formatted files - with CDS features for the latter - representing bacterial genomes or metagenomes.
For eukaryotic genomes full GenBank format with CDS features are expected; however, FASTA formatted assemblies may instead be provided if a "reference proteome" is provided.
Check out example commands for prepTG on the 4. basic usage examples wiki page.
For bacterial genomes or bacterial metagenomes, users are able to use pyrodigal (default) or prodigal to perform de novo gene calling. More recently, we also have the availability of prodigal-gv as an option for gene-calling when phages are the gene clusters of interest.
For eukaryotic genomes, users are able to map a high-quality gene-calling prediction for some reference genome to the remainder of the genomes. This approach is generally recommended only for single-species investigations and has only been tested with microbial eukaryotic genomes of a modest size (e.g. fungii, not gigantic genomes such as those of plants).
usage: prepTG [-h] [-d DOWNLOAD_PREMADE] [-i INPUT_DIR] [-g GTDB_TAXON] -o OUTPUT_DIR [-l LOCUS_TAG_LENGTH] [-r] [-gcm GENE_CALLING_METHOD] [-m] [-rp REFERENCE_PROTEOME] [-cst] [-c CPUS]
[-mm MAX_MEMORY] [-v]
Program: prepTG
Author: Rauf Salamzade
Affiliation: Kalan Lab, UW Madison, Department of Medical Microbiology and Immunology
Prepares a directory of target genomes for being searched for query gene clusters using fai.
Premade databases of representative genomes are available for the following genera:
Acinetobacter (n=1,643), Bacillales (n=3,150), Corynebacterium (n=726), Enterobacter (n=878),
Enterococcus (n=937), Escherichia (n=2,436), Klebsiella (n=1,022), Listeria (n=353),
Mycobacterium (n=744), Pseudomonas (n=2,666), Salmonella (n=308), Staphylococus (n=496),
Streptomyces (n=1,555), Streptococcus (n=2,452), Cutibacterium (n=27), Neisseria (n=414),
Lactobacillus (n=541), and Micromonospora (n=211).
In addition, users can simply request all genomes belonging to a specific species/genus
in GTDB R214 to be downloaded.
----------------------------------------------------------------------------------------
> Example commands:
1. Setup a prepTG database which includes some local genomes and all Cutibacterium granulosum
genomes:
prepTG -i User_Genomes_Directory/ -g "Cutibacterium granulosum" -o prepTG_Database/
2. Setup local prepTG database by downloading a premade one of representative
Cutibacterium genomes:
prepTG -d Cutibacterium -o prepTG_Database/
----------------------------------------------------------------------------------------
> Considerations
If FASTA format is provided, assumption is that genomes are prokaryotic and
pyrodigal/prodigal will be used to perform gene-calling. Eukaryotic genomes can
be provided as FASTA format but the --reference_proteome file should be used in
such case to map proteins from a reference proteome (from the same species ideally)
on to the target genomes. This will prevent detection of new genes in gene-clusters
detected by fai but synchronize gene-calling and allow for better similarity
assessment between orthologous genes.
options:
-h, --help show this help message and exit
-d DOWNLOAD_PREMADE, --download_premade DOWNLOAD_PREMADE
Download and setup pre-made databases of representative genomes for specific taxon/genus.
Provide name of the taxon, e.g. "Escherichia"
-i INPUT_DIR, --input_dir INPUT_DIR
Directory with target genomes (either featuring GenBanks or FASTAs).
-g GTDB_TAXON, --gtdb_taxon GTDB_TAXON
Name of a GTDB-R214 valid genus or species, should be surrounded by
quotes (e.g. "Escherichia coli").
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Output directory, which can then be provided as input for the
"-tg" argument in fai.
-l LOCUS_TAG_LENGTH, --locus_tag_length LOCUS_TAG_LENGTH
Length of locus tags to set. Default is 3, allows for <~18k genomes.
-r, --rename_locus_tags
Whether to rename locus tags if provided for CDS features in GenBanks.
-gcm GENE_CALLING_METHOD, --gene_calling_method GENE_CALLING_METHOD
Method to use for gene calling. Options are: pyrodigal, prodigal,
or prodigal-gv. [Default is pyrodigal].
-m, --meta_mode Flag to use meta mode instead of single for pyrodigal/prodigal.
-rp REFERENCE_PROTEOME, --reference_proteome REFERENCE_PROTEOME
Provide path to a reference proteome to use for protein/gene-calling
in target genomes - which should be in FASTA format.
-cst, --create_species_tree
Use skani to infer a neighbor-joing based species tree for the genomes.
-c CPUS, --cpus CPUS Total number of cpus/threads to use for running OrthoFinder2/prodigal.
[Default is 1].
-mm MAX_MEMORY, --max_memory MAX_MEMORY
Uses resource module to set soft memory limit. Provide in Giga-bytes.
Generally memory shouldn't be a major concern unless working
with hundreds of large metagenomes. [currently
experimental; default is None].
-v, --version Get version and exit.