.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH KMA "1" "February 2019" "kma 1.1.7" "User Commands"
.SH NAME
kma \- mapps raw reads to a template database
.SH DESCRIPTION
mapps raw reads to a template database.
.SH OPTIONS
.TP
\fB\-o\fR
Output file                     None            REQUIRED
.TP
\fB\-t_db\fR
Template DB                     None            REQUIRED
.TP
\fB\-i\fR
Input file name(s)              STDIN
.TP
\fB\-ipe\fR
Input paired end file name(s)
.TP
\fB\-int\fR
Input interleaved file name(s)
.TP
\fB\-k\fR
Kmersize                        DB defined
.TP
\fB\-e\fR
evalue                          0.05
.TP
\fB\-ConClave\fR
ConClave version                1
.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\-ef\fR
Print additional features       False
.TP
\fB\-vcf\fR
Make vcf file, 2 to apply FT    False/0
.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\-a\fR
Print all best mappings         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
Only count kmers                False
.TP
\fB\-Mt1\fR
Map only to "num" template.     0 / False
.TP
\fB\-ID\fR
Minimum ID                      1.0%
.TP
\fB\-ss\fR
Sparse sorting (q,c,d)          q
.TP
\fB\-pm\fR
Pairing method (p,u,f)          u
.TP
\fB\-fpm\fR
Fine Pairing method (p,u,f)     u
.TP
\fB\-apm\fR
Sets both pm and fpm            u
.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\-ck\fR
Count kmers instead of
pseudo alignment                False
.TP
\fB\-ca\fR
Make circular alignments        False
.TP
\fB\-boot\fR
Bootstrap sequence              False
.TP
\fB\-bc\fR
Base calls should be
significantly overrepresented.  [True]
.TP
\fB\-bc90\fR
Base calls should be both
significantly overrepresented,
and have 90% agreement.         False
.TP
\fB\-bcNano\fR
Call bases at suspicious
deletions, made for nanopore.   False
.TP
\fB\-and\fR
Both mrs and p_value thresholds
has to reached to in order to
report a template hit.          or
.TP
\fB\-mq\fR
Minimum mapping quality         0
.TP
\fB\-mrs\fR
Minimum alignment score,
normalized to alignment length  0.50
.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\-per\fR
Reward for pairing reads        7
.TP
\fB\-cge\fR
Set CGE penalties and rewards   False
.TP
\fB\-t\fR
Number of threads               1
.TP
\fB\-v\fR
Version
.TP
\fB\-h\fR
Shows this help message
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.