updated README with updated usage data

phac-nml · Sep 26, 2024 · 0956002 · 0956002
1 parent df32c12
commit 0956002
Showing 1 changed file with 58 additions and 58 deletions.
diff --git a/README.rst b/README.rst
@@ -127,7 +127,7 @@ SISTR will automatically initialize database of *Salmonella* serovar determinati
 The SISTR database v1.3 got minor updates by collapsing some of the serovars detailed in ``CHANGELOG.md`` file
 
 - SISTR v1.1 database is available at https://zenodo.org/records/13618515 or via a direct url https://zenodo.org/records/13618515/files/SISTR_V_1.1_db.tar.gz?download=1
-- SISTR v1.3 database is available at https://zenodo.org/records/13693495 or via a direct url https://zenodo.org/records/13693495/files/SISTR_V_1.1.3_db.tar.gz?download=1
+- SISTR v1.3 database is available at https://zenodo.org/records/13693495 or va a direct url https://zenodo.org/records/13693495/files/SISTR_V_1.1.3_db.tar.gz?download=1
 
 
 Dependencies
@@ -171,66 +171,66 @@ If you run ``sistr -h``, you should see the following usage info:
                  [-l [LIST_OF_SEROVARS]] [-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.
+	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:
+	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.
 
-If you find this program useful in your research, please cite as:
-
-The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies.
-Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada.
-PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
-
-positional arguments:
-  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
-
+	If you find this program useful in your research, please cite as:
+
+	The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies.
+	Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada.
+	PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
+
+	positional arguments:
+	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
+	
 
 Example Usage
 -------------