Ubuntu Manpage: srst2 - Short Read Sequence Typer

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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.