NAME

       srst2 - 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 (minouye@unimelb.edu.au), Harriet  Dashnow  (h.dashnow@gmail.com),  Kathryn
       Holt (kholt@unimelb.edu.au), Bernie Pope (bjpope@unimelb.edu.au)

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