-h, --help
show this help message and exit
--version
show program's version number and exit
--input_se INPUT_SE [INPUT_SE ...]
Single end read file(s) for analysing (may be gzipped)
--input_pe INPUT_PE [INPUT_PE ...]
Paired end read files for analysing (may be gzipped)
--merge_paired
Switch on if all the input read sets belong to a single sample, and you want to merge their data
to get a single result
--forward FORWARD
Designator for forward reads (only used if NOT in MiSeq format sample_S1_L001_R1_001.fastq.gz;
otherwise default is _1, i.e. expect forward reads as sample_1.fastq.gz)
--reverse REVERSE
Designator for reverse reads (only used if NOT in MiSeq format sample_S1_L001_R2_001.fastq.gz;
otherwise default is _2, i.e. expect forward reads as sample_2.fastq.gz
--read_type {q,qseq,f}
Read file type (for bowtie2; default is q=fastq; other options: qseq=solexa, f=fasta).
--mlst_db MLST_DB
Fasta file of MLST alleles (optional)
--mlst_delimiter MLST_DELIMITER
Character(s) separating gene name from allele number in MLST database (default "-", as in arcc-1)
--mlst_definitions MLST_DEFINITIONS
ST definitions for MLST scheme (required if mlst_db supplied and you want to calculate STs)
--mlst_max_mismatch MLST_MAX_MISMATCH
Maximum number of mismatches per read for MLST allele calling (default 10)
--gene_db GENE_DB [GENE_DB ...]
Fasta file/s for gene databases (optional)
--no_gene_details
Switch OFF verbose reporting of gene typing
--gene_max_mismatch GENE_MAX_MISMATCH
Maximum number of mismatches per read for gene detection and allele calling (default 10)
--min_coverage MIN_COVERAGE
Minimum %coverage cutoff for gene reporting (default 90)
--max_divergence MAX_DIVERGENCE
Maximum %divergence cutoff for gene reporting (default 10)
--min_depth MIN_DEPTH
Minimum mean depth to flag as dubious allele call (default 5)
--min_edge_depth MIN_EDGE_DEPTH
Minimum edge depth to flag as dubious allele call (default 2)
--prob_err PROB_ERR
Probability of sequencing error (default 0.01)
--stop_after STOP_AFTER
Stop mapping after this number of reads have been mapped (otherwise map all)
--other OTHER
Other arguments to pass to bowtie2 (must be escaped, e.g. "\--no-mixed".
--mapq MAPQ
Samtools -q parameter (default 1)
--baseq BASEQ
Samtools -Q parameter (default 20)
--samtools_args SAMTOOLS_ARGS
Other arguments to pass to samtools mpileup (must be escaped, e.g. "\-A").
--output OUTPUT
Prefix for srst2 output files
--log Switch ON logging to file (otherwise log to stdout)
--save_scores
Switch ON verbose reporting of all scores
--report_new_consensus
If a matching alleles is not found, report the consensus allele. Note, only SNP differences are
considered, not indels.
--report_all_consensus
Report the consensus allele for the most likely allele. Note, only SNP differences are considered,
not indels.
--use_existing_pileup
Use existing pileups if available, otherwise they will be generated
--use_existing_scores
Use existing scores files if available, otherwise they will be generated
--keep_interim_alignment
Keep interim files (sam & unsorted bam), otherwise they will be deleted after sorted bam is
created
--prev_output PREV_OUTPUT [PREV_OUTPUT ...]
SRST2 results files to compile (any new results from this run will also be incorporated)
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