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SRST2 (version 0.3.7)
SRST2.1 default value is 10 however our testing indicates that the value should be set to 250 to prevent erroneous allele calls.
Typically _ or -

What it does

Short Read Sequence Typing for Bacterial Pathogens

This program is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes. The tool has a database of virulence factors that was extracted from http://www.mgc.ac.cn/VFs/ .

For more information about SRST2 and for instructions on how to format custom databases, visit https://github.com/katholt/srst2

Usage

Basic Options

Read Type
  • Single-end: Single end read file(s) for analysing (--input_se)
  • Paired-end: Paired end read file(s) for analysing (--input_pe)
Job Type
  • MLST only: Reports Sequence Types
  • MLST and VFDB: Reports Sequence Types and user can choose one of the built-in Virulence Factor Datebase (VFDB) strains
  • MLST and custom database: Reports Sequence Types and user can upload their own custom database
  • VFDB only: Use can choose one of the built-in Virulence Factor Databasse (VFDB) strains
  • Custom database only: Use can upload their own custom database
ST definitions for MLST scheme:
  • Required if you want to calculate STs (--mlst_definitions)
Fasta file of MLST alleles:
  • Required if you want to calculate STs (--mlst_db)
Fasta file for gene database:
  • Required if you want details of the sequences. The user must provide their own database (--gene_db)
VFDB strain:
  • Required if you want details of the sequences. The use may choose one of the listed strains (--gene_db)
Read file type:
  • fastq
  • solexa
  • fasta
Character(s) separating gene name from allele number in MLST database:
  • Required for all MLST job types
  • Typically either _ or -
  • The output from getMLST will identify the delimiter.
Maximum number of mismatches per read for MLST allele calling:
  • Required for all MLST job types
  • For MLST schemas with inserts this number should be set to a high value (recommended: 250)
Maximum number of mismatches per read for gene allele calling:
  • Required for all VDFB or custom database job types
  • For genes with inserts this number should be set to a high value (recommended: 250).
Option Type:
  • Basic: Includes only the options listed above
  • Advanced: Includes the options listed below

Advanced Options

Minimum %coverage cutoff for gene reporting:
  • Default is 90 (--min_coverage)
Maximum %divergence cutoff for gene reporting:
  • Default is 10 (--max_divergence)
Minimum mean depth to flag as dubious allele call:
  • Default is 5 (--min_depth)
Minimum edge depth to flag as dubious allele call:
  • Default is 2 (--min_edge_depth)
Probability of sequencing error:
  • Default is 0.01 (--prob_err)
Stop mapping after this number of reads have been mapped (otherwise map all):
  • Default maps all (--stop_after)
Other arguments to pass to bowtie2:
--other
Samtools -q parameter:
  • Default is 1 (--mapq)
Samtools -Q parameter:
  • Default is 20 (--baseq)
Bowtie2 -I/--minins:
  • The minimum fragment length for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates.
  • The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.
  • Default: 0 (essentially imposing no minimum)
Bowtie2 -X/--maxins:
  • The maximum fragment length for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates.
  • The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.
  • Default: 500.
Acknowledgments

Original Author: Mariam Iskander

Jen Cabral

Philip Mabon

Mark Iskander

Eric Enns