indexer

Synopsis

indexer [OPTIONS] -c

Description

STing indexer creates indexes (DBs) required by the STing typer and detector programs for loci-based typing analysis and detecting genes, respectively, from NGS raw sequence reads.

-h, --help

Display the help message.

--version

Display version information.

-c, --config-file CONFIG_FILE

A tab delimited file whith names and paths to the typing scheme files (see the FILE FORMAT DETAILS section below).

-p, --db-prefix PREFIX

Filename prefix for the DB files to be created. You can specify a folder structure here to store your DB at a particular location, e.g., path/to/my/db/prefix. Default: name of the config file CONFIG_FILE

-m, --mode MODE

Indexing mode. Valid options: MLST, GDETECT. Select MLST to create a database for MLST analysis or GDETECT to create a database for gene detection. Default: _MLST_.

File format details

CONFIG_FILE

A tab separated file with the name and location of files for creating a DB. Config files for MLST DBs (MLST mode) must have two sections: [loci] that describes names and paths to alleles sequence files for each locus, and [profile] that describes the name and path to the profile file. Config files for gene detection DBs (GDETECT mode), only require the [loci] section. An example of a config file for a MLST DB is as follows:

[loci] locus1 relative/path/to/locusFile1 locus2 relative/path/to/locusFile2 locusN relative/path/to/locusFileN [profile] profile relative/path/to/profileFile

Paths are relative to the config file itself. Blank lines and comments (lines starting with '#') will be ignored.

Allele sequence file

A standard multi-FASTA file (.fa or .fasta) in which each sequence description must be the locus name and the allele number separated by '_':

```

abcZ_1 TTTGATACTGTTGCCGA... abcZ_2 TTTGATACTGTTGCCGA... ```

Profile file

A tab separated file that contains the ST and the corresponding allelic profile:

ST abcZ adk aroE fumC gdh pdhC pgm clonal_complex 1 1 3 1 1 1 1 3 ST-1 complex/subgroup I/II 2 1 3 4 7 1 1 3 ST-1 complex/subgroup I/II 3 1 3 1 1 1 23 13 ST-1 complex/subgroup I/II 4 1 3 3 1 4 2 3 ST-4 complex/subgroup IV