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updated README with updated usage data
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@kbessonov1984
kbessonov1984 committed Sep 26, 2024
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Expand Up @@ -165,18 +165,18 @@ If you run ``sistr -h``, you should see the following usage info:
.. code-block:: none
usage: sistr_cmd [-h] [-i fasta_path genome_name] [-f OUTPUT_FORMAT]
[-o OUTPUT_PREDICTION] [-M] [-p CGMLST_PROFILES]
[-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
[--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
[-l [LIST_OF_SEROVARS]] [-v] [-V]
[F [F ...]]
[-o OUTPUT_PREDICTION] [-p CGMLST_PROFILES]
[-n NOVEL_ALLELES] [-a ALLELES_OUTPUT] [-T TMP_DIR] [-K]
[--use-full-cgmlst-db] [--no-cgmlst] [-m] [--qc] [-t THREADS]
[-v] [-V]
[F [F ...]]
SISTR (Salmonella In Silico Typing Resource) Command-line Tool
==============================================================
Serovar predictions from whole-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
Note about using the "--use-full-cgmlst-db" flag:
The "centroid" allele database is ~10% the size of the full set so analysis is much quicker with the "centroid" vs "full" set of alleles. Results between 2 cgMLST allele sets should not differ.
The "centroid" allele database is ~10% the size of the full set so analysis is much quicker with the "centroid" vs "full" set of alleles. Results between 2 cgMLST allele sets should not differ.
If you find this program useful in your research, please cite as:
Expand All @@ -185,52 +185,49 @@ If you run ``sistr -h``, you should see the following usage info:
PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
positional arguments:
F Input genome FASTA file
F Input genome FASTA file
optional arguments:
-h, --help show this help message and exit
-i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name
fasta file path to genome name pair
-f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
Output format (json, csv, tab, pickle)
-o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
SISTR serovar prediction output path
-M, --more-results Output more detailed results (-M) and all antigen
search blastn results (-MM)
-p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
Output CSV file destination for cgMLST allelic
profiles
-n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
Output FASTA file destination of novel cgMLST alleles
from input genomes
-a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT
Output path of allele sequences and info to JSON
-T TMP_DIR, --tmp-dir TMP_DIR
Base temporary working directory for intermediate
analysis files.
-K, --keep-tmp Keep temporary analysis files.
--use-full-cgmlst-db Use the full set of cgMLST alleles which can include
highly similar alleles. By default the smaller
"centroid" alleles or representative alleles are used
for each marker.
--no-cgmlst Do not run cgMLST serovar prediction
-m, --run-mash Determine Mash MinHash genomic distances to Salmonella
genomes with trusted serovar designations. Mash binary
must be in accessible via $PATH (e.g. /usr/bin).
--qc Perform basic QC to provide level of confidence in
serovar prediction results.
-t THREADS, --threads THREADS
Number of parallel threads to run sistr_cmd analysis.
-l [LIST_OF_SEROVARS], --list-of-serovars [LIST_OF_SEROVARS]
A path to a single column text file containing list of
serovar(s) to check serovar prediction against. Report
predicted serovar in "serovar_in_serovar_list" field
as Y (present) and N (absent) in the list. The default
list will be used if not file specified.
-v, --verbose Logging verbosity level (-v == show warnings; -vvv ==
show debug info)
-V, --version show program's version number and exit
-h, --help show this help message and exit
-i fasta_path genome_name, --input-fasta-genome-name fasta_path genome_name
fasta file path to genome name pair
-f OUTPUT_FORMAT, --output-format OUTPUT_FORMAT
Output format (json, csv, pickle)
-o OUTPUT_PREDICTION, --output-prediction OUTPUT_PREDICTION
SISTR serovar prediction output path
-p CGMLST_PROFILES, --cgmlst-profiles CGMLST_PROFILES
Output CSV file destination for cgMLST allelic
profiles
-n NOVEL_ALLELES, --novel-alleles NOVEL_ALLELES
Output FASTA file destination of novel cgMLST alleles
from input genomes
-a ALLELES_OUTPUT, --alleles-output ALLELES_OUTPUT
Output path of allele sequences and info to JSON
-T TMP_DIR, --tmp-dir TMP_DIR
Base temporary working directory for intermediate
analysis files.
-K, --keep-tmp Keep temporary analysis files.
--use-full-cgmlst-db Use the full set of cgMLST alleles which can include
highly similar alleles. By default the smaller
"centroid" alleles or representative alleles are used
for each marker.
--no-cgmlst Do not run cgMLST serovar prediction
-m, --run-mash Determine Mash MinHash genomic distances to Salmonella
genomes with trusted serovar designations. Mash binary
must be in accessible via $PATH (e.g. /usr/bin).
--qc Perform basic QC to provide level of confidence in
serovar prediction results.
-t THREADS, --threads THREADS
Number of parallel threads to run sistr_cmd analysis.
-l LIST_OF_SEROVARS, --list-of-serovars LIST_OF_SEROVARS
A path to a single column text file containing list of
serovar(s) to check serovar prediction against. Report
predicted serovar is Y (present) and N (absent) in the
list
-v, --verbose Logging verbosity level (-v == show warnings; -vvv ==
show debug info)
-V, --version show program's version number and exit
Example Usage
-------------
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