.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH KMERRESISTANCE "1" "June 2018" "kmerresistance 2.0+git20180205.26467e9" "User Commands"
.SH NAME
kmerresistance \- correlates mapped genes with the predicted species of WGS samples
.SH SYNOPSIS

.SH 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.
.SH OPTIONS
.TP
\fB\-i\fR
Input/query file name                                   REQUIRED
.TP
\fB\-o\fR
Output file                                             REQUIRED
.TP
\fB\-t_db\fR
Template DB                                             REQUIRED
.TP
\fB\-s_db\fR
Species DB                                              REQUIRED
.TP
\fB\-id\fR
ID threshhold                   70.0
.TP
\fB\-dct\fR
Depth correction threshhold     0.1
.TP
\fB\-kma\fR
alternative KMA         kma
.SS KMA options:
.TP
\fB\-i\fR
Input/query file name           None            REQUIRED
.TP
\fB\-o\fR
Output file                     None            REQUIRED
.TP
\fB\-t_db\fR
Template DB                     None            REQUIRED
.TP
\fB\-k\fR
Kmersize                        16
.TP
\fB\-e\fR
evalue                          0.05
.TP
\fB\-delta\fR
Align in pieces of delta        511
.TP
\fB\-mem_mode\fR
Use kmers to choose best
template, and save memory       False
.TP
\fB\-ex_mode\fR
Searh kmers exhaustively        False
.TP
\fB\-deCon\fR
Remove contamination            False
.TP
\fB\-dense\fR
Do not allow insertions
in assembly                     False
.TP
\fB\-ref_fsa\fR
Consensus sequnce will
have "n" instead of gaps        False
.TP
\fB\-matrix\fR
Print assembly matrix           False
.TP
\fB\-mp\fR
Minimum phred score             30
.TP
\fB\-5p\fR
Cut a constant number of
nucleotides from the 5 prime.   0
.TP
\fB\-Sparse\fR
Run KmerFinder                  False
.TP
\fB\-ID\fR
Minimum ID                      1.0%
.TP
\fB\-ss\fR
Sparse sorting (q,c,d)          q
.TP
\fB\-shm\fR
Use shared DB made by kma_shm   0 (lvl)
.TP
\fB\-swap\fR
Swap DB to disk                 0 (lvl)
.TP
\fB\-1t1\fR
Skip HMM                        False
.TP
\fB\-boot\fR
Bootstrap sequence              False
.TP
\fB\-mrs\fR
Minimum alignment score,
normalized to alignment length  0.5
.TP
\fB\-reward\fR
Score for match                 1
.TP
\fB\-penalty\fR
Penalty for mismatch            \fB\-2\fR
.TP
\fB\-gapopen\fR
Penalty for gap opening         \fB\-3\fR
.TP
\fB\-gapextend\fR
Penalty for gap extension       \fB\-1\fR
.TP
\fB\-h\fR
Shows this help message
.SH EXAMPLES
Mapping reads against resistance genes:
.IP
  kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder -s_db bacteria
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.