How to search with FlexTyper

Cmd Line:

You can display the input options using

Usage: ../build/flextyper [options] outputFile
Description: flextyper enables the user to quickly search for kmers inside the FmIndex
 
Options:
  -h, --help              Displays this help.
  -v, --verbose           prints debugging messages
  -c, --config <file>     ini file to use
  -k, --kmerSize <value>  kmer size
  -s, --stride <value>    stride
  -m, --maxOcc <value>    maxOcc
  -u, --unique            ignore nonunique kmers
 
Arguments:
  outputFile              fm9 dataset

Setting.ini

The settings file contains all the parameters for the search.

Setting Ini File

Example 1: Viral Detection

viralsearchexample

Example 2: SNV Detection

snvsearchexample