NAME

       kmerresistance - correlates mapped genes with the predicted species of WGS samples

SYNOPSIS

DESCRIPTION

       KmerResistance  correlates  mapped  genes with the predicted species of WGS samples, where
       this this allows for identification of genes in samples which have been  poorly  sequenced
       or  high  accuracy  predictions  for  samples  with  contamination. KmerResistance has one
       dependency, namely KMA to perform the mapping, which is also freely available.

OPTIONS

       -i     Input/query file name                                   REQUIRED

       -o     Output file                                             REQUIRED

       -t_db  Template DB                                             REQUIRED

       -s_db  Species DB                                              REQUIRED

       -id    ID threshhold                   70.0

       -dct   Depth correction threshhold     0.1

       -kma   alternative KMA         kma

   KMA options:
       -i     Input/query file name           None            REQUIRED

       -o     Output file                     None            REQUIRED

       -t_db  Template DB                     None            REQUIRED

       -k     Kmersize                        16

       -e     evalue                          0.05

       -delta Align in pieces of delta        511

       -mem_mode
              Use kmers to choose best template, and save memory       False

       -ex_mode
              Searh kmers exhaustively        False

       -deCon Remove contamination            False

       -dense Do not allow insertions in assembly                     False

       -ref_fsa
              Consensus sequnce will have "n" instead of gaps        False

       -matrix
              Print assembly matrix           False

       -mp    Minimum phred score             30

       -5p    Cut a constant number of nucleotides from the 5 prime.   0

       -Sparse
              Run KmerFinder                  False

       -ID    Minimum ID                      1.0%

       -ss    Sparse sorting (q,c,d)          q

       -shm   Use shared DB made by kma_shm   0 (lvl)

       -swap  Swap DB to disk                 0 (lvl)

       -1t1   Skip HMM                        False

       -boot  Bootstrap sequence              False

       -mrs   Minimum alignment score, normalized to alignment length  0.5

       -reward
              Score for match                 1

       -penalty
              Penalty for mismatch            -2

       -gapopen
              Penalty for gap opening         -3

       -gapextend
              Penalty for gap extension       -1

       -h     Shows this help message

EXAMPLES

       Mapping reads against resistance genes:

                kmerresistance -i sample_1.fastq sample_2.fastq  -o  out  -t_db  ResFinder  -s_db
              bacteria

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.