Documentation¶

Usage:¶

ngm [-c ] -q  -r  -o 
 [parameter]

Options:

Input/Output:

  -c/--config <path>            Path to the config file. The config file contains all advanced options.
                                If this parameter is omitted, default values will be used.
  -r/--reference <path>         Path or ID of the reference genome (fasta/fastq).
  -q/--query <path>             Path to the read file (fasta/fastq). If the query file is omitted,
                                NGM will only preprocess the reference.
  -p/--paired                   Input data is paired end. (default: off)
  -o/--output <path>            Path to output file.

General:
  -t/--threads <int>            Number of candidate search threads
  -s/--sensitivity [0-1]        Higher values equal lower sensitivity. (default: estimated)
  -g/--gpu <int>                Number of GPUs used for alignment computation. (default: 0)
  --bs-mapping                  Enables bisulfite mapping (For bs-mapping kmer-skip will be applied to
                                the reads instead of the reference sequence).  
  -h/--help                     Prints help and aborts program

Advanced settings:

  -k/--kmer [10-14]             Kmer length in bases. (default: 13)
  --kmer-skip <int>             Number of k-mers to skip when building the lookup table from
                                the reference(default: 2)
 -m/mode [0|1]                  Alignment mode: 0 = local, 1 = semi-global. (default: 0)
 --corridor <int>               Width of SW corridor (default: 15)

Known issues¶

The NGM alignment libraries currently don't work with the AMD APP SDK 2.6.