srst2(1) Short Read Sequence Typer

SYNOPSIS

srst2 [-h] [--version] [--input_se INPUT_SE [INPUT_SE ...]] [--input_pe INPUT_PE [INPUT_PE ...]] [--merge_paired] [--forward FORWARD] [--reverse REVERSE] [--read_type {q,qseq,f}] [--mlst_db MLST_DB] [--mlst_delimiter MLST_DELIMITER] [--mlst_definitions MLST_DEFINITIONS] [--mlst_max_mismatch MLST_MAX_MISMATCH] [--gene_db GENE_DB [GENE_DB ...]] [--no_gene_details] [--gene_max_mismatch GENE_MAX_MISMATCH] [--min_coverage MIN_COVERAGE] [--max_divergence MAX_DIVERGENCE] [--min_depth MIN_DEPTH] [--min_edge_depth MIN_EDGE_DEPTH] [--prob_err PROB_ERR] [--stop_after STOP_AFTER] [--other OTHER] [--mapq MAPQ] [--baseq BASEQ] [--samtools_args SAMTOOLS_ARGS] --output OUTPUT [--log] [--save_scores] [--report_new_consensus] [--report_all_consensus] [--use_existing_pileup] [--use_existing_scores] [--keep_interim_alignment] [--prev_output PREV_OUTPUT [PREV_OUTPUT ...]]

DESCRIPTION

SRST2 - Short Read Sequence Typer (v2)

OPTIONS

-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)

EXAMPLE

Assume you have a database downloaded by getmlst(1) by using
getmlst --species "Escherichia coli#1"

For SRST2, remember to check what separator is being used in this allele database

Looks like --mlst_delimiter '-'


  >adk-1  --> -->   ('adk', '-', '1')

Suggested srst2 command for use with this MLST database:

srst2 --output test --input_pe *.fastq.gz --mlst_db Escherichia_coli#1.fasta --mlst_definitions ecoli.txt --mlst_delimiter '-'

Note, this is correctly guessing that we should use the default --mlst_delimiter '-' with this database. The log file will tell you exactly what files were downloaded.

More verbose example usage is described in /usr/share/doc/srst2/example.txt.gz

AUTHOR

Michael Inouye ([email protected]), Harriet Dashnow ([email protected]), Kathryn Holt ([email protected]), Bernie Pope ([email protected])

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.