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KMA_INDEX(1) User Commands KMA_INDEX(1)

NAME

kma_index - creates the databases needed to run KMA, from a list of fasta files given

DESCRIPTION

kma_index creates the databases needed to run KMA, from a list of fasta files given.

OPTIONS

-i
Input/query file name (STDIN: "--") None
-o
Output file Input/template file
-batch
Batch input file
-deCon
File with contamination (STDIN: "--") None/False
-batchD
Batch decon file
-t_db
Add to existing DB None/False
-k
Kmersize 16
-k_t
Kmersize for template identification 16
-k_i
Kmersize for indexing 16
-ML
Minimum length of templates kmersize (16)
-CS
Start Chain size 1 M
-ME
Mega DB False
-NI
Do not dump *.index.b False
-Sparse
Make Sparse DB ('-' for no prefix) None/False
-ht
Homology template 1.0
-hq
Homology query 1.0
-and
Both homolgy thresholds has to be reached or
-v
Version
-h
Shows this help message

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
February 2019 kma_index 1.1.7