.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH KMA_INDEX "1" "February 2019" "kma_index 1.1.7" "User Commands"
.SH NAME
kma_index \- creates the databases needed to run KMA, from a list of fasta files given
.SH DESCRIPTION
kma_index creates the databases needed to run KMA, from a list of fasta files given.
.SH OPTIONS
.TP
\fB\-i\fR
Input/query file name (STDIN: "\-\-")     None
.TP
\fB\-o\fR
Output file                             Input/template file
.TP
\fB\-batch\fR
Batch input file
.TP
\fB\-deCon\fR
File with contamination (STDIN: "\-\-")   None/False
.TP
\fB\-batchD\fR
Batch decon file
.TP
\fB\-t_db\fR
Add to existing DB                      None/False
.TP
\fB\-k\fR
Kmersize                                16
.TP
\fB\-k_t\fR
Kmersize for template identification    16
.TP
\fB\-k_i\fR
Kmersize for indexing                   16
.TP
\fB\-ML\fR
Minimum length of templates             kmersize (16)
.TP
\fB\-CS\fR
Start Chain size                        1 M
.TP
\fB\-ME\fR
Mega DB                                 False
.TP
\fB\-NI\fR
Do not dump *.index.b                   False
.TP
\fB\-Sparse\fR
Make Sparse DB ('\-' for no prefix)      None/False
.TP
\fB\-ht\fR
Homology template                       1.0
.TP
\fB\-hq\fR
Homology query                          1.0
.TP
\fB\-and\fR
Both homolgy thresholds
has to be reached                       or
.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.