CorGE Usage Guide
Options
CorGE
usage: CorGE [-h] {collect_genomes,extract_genes} …
- positional arguments:
- {collect_genomes,extract_genes}
Subcommands
collect_genomes Collect nucleotide- and protein-encoded genomes of interest extract_genes Extract SCCGs from all collected genomes and curate data for tree building
CorGE collect_genomes
usage: CorGE collect_genomes [-h] [–all] [–ncbi_species NCBI_SPECIES] [–ncbi_accessions NCBI_ACCESSIONS] [–local LOCAL] [–outgroup OUTGROUP] [-n] output_dir
- positional arguments:
output_dir Directory to collect genomes in
- options:
- -h, --help
show this help message and exit
- --all
Collect one representative genome from each species listed in NCBI’s RefSeq database. Don’t use this with –ncbi_species, –ncbi_accessions, or –local
- --ncbi_species NCBI_SPECIES
File listing species level taxon ids to be collected from NCBI
- --ncbi_accessions NCBI_ACCESSIONS
File listing genome accessions to be collected from NCBI
- --local LOCAL
Directory containing nucleotide- and protein-encoded pairs of genome files. Any unpaired files will be ignored
- --outgroup OUTGROUP
Specify the outgroup for tree rooting. Integers will be parsed as species level taxon ids and retrieved from NCBI. Otherwise will search for a matching nucleotide-encoded file in ouput_dir or local (Default: 2173, enter None to not use outgroup rooting)
- -n
Dry run, show what would be gathered but don’t do it
CorGE extract_genes
usage: CorGE extract_genes [-h] [-o OUTPUT] [-t {prot,nucl}] [-n {acc,txid,strain,species}] genomes
- positional arguments:
genomes Directory with collected genomes (curated with collect_genomes)
- options:
- -h, --help
show this help message and exit
- -o OUTPUT, --output OUTPUT
Directory to write output to (Default: ./)
- -t {prot,nucl}, –type {prot,nucl}
Output in merged-sequences can be nucleotide- or protein-encoded (Default: prot)
- -n {acc,txid,strain,species}, –name {acc,txid,strain,species}
Names to show on final tree (Default: txid)
collect_genomes
This is the command for retrieving genomes for all of the bacteria you want in your tree, from NCBI, a local directory, or both. CorGE does all of its work with pairs of files: a protein-encoded genome (usually saved with a .faa extension) and a nucleotide-encoded genome (usually saved with a .fna extension). These files have the same name but different extensions with the name for any NCBI files being the genome accession (e.g. “GCF_000218545”) and the name for any local files being preserved.
Tip
Especially when downloading lots of genomes, it’s always a good idea to run your command with the dryrun option (-n) first. This will print out what it’s planning to do without doing it, so you can verify that it will do the right thing.
Common Use Cases
To collect a set of representative/reference genomes for a list of species, create a file of species-level taxon ids, one id per line, and pass that file to CorGE:
CorGE collect_genomes . --ncbi_species species_list.txt
Tip
If you don’t care about rooting the final tree, you can specify –outgroup None. The pipeline will still use a midpoint algorithm to root the final tree, but the input to that step will be the unrooted tree.
To collect one genome for each species NCBI has, use the –all option:
CorGE collect_genomes /path/to/db --all
Suppose you want to create a strain level tree from some existing NCBI E. coli genomes and some that you have locally and then root that tree with a reference Clostridium botulinum genome. You create a list of the genome accessions you want to collect (same as species taxa, one accession per line in a text file) and run:
CorGE collect_genomes ecoli-db/ --ncbi_accessions accession_list.txt
This will collect each of those genomes and put them in ecoli-db/ (as well as grabbing Methanobrevibacter smithii in the outgroup dir, this will be overwritten by the next step). Next we need to get all the local files in there, but we need them to follow a couple rules: 1) only pairs of files will be collected so every nucleotide file should have a paired protein file with the same name (e.g. example.fna and example.faa) and 2) the annotations for the protein files should have a unique name as the first space-separated piece of the annotation and then corresponding sequences in the nucleotide files should have annotations that contain that name (e.g. first protein sequence is annotated with > example00001 description and so on and corresponding nucleotide sequence is annotated with > WXK40_example00001_DEADBEEF). Provided they are in compliance with the above and all in one directory run:
CorGE collect_genomes ecoli-db/ --local assembled-genomes/ --outgroup 1491
This should leave you with all your files organized into ecoli-db/protein, ecoli-db/nucleotide, and ecoli-db/outgroup directories.
Tip
You could also do this all in one command CorGE collect_genomes ecoli-db/ –ncbi_accessions accession_list.txt –local assembled-genomes/ –outgroup 1491
extract_genes
To curate genes for a multi-species bacteria tree run:
CorGE extract_genes /path/to/db
Continuing the example from the last section, to curate genes for this strain level E. coli tree, run:
CorGE extract_genes ecoli-db/ --type nucl --name strain
This will prepare you to build a nucleotide based tree of E. coli strains where the leaf names will be either the strain name (if it came from NCBI) or the file name (if it was local).