kma_index1

Overview

kma_index creates the databases needed to run KMA, from a list of fasta files given. Options are: Desc: Default:

-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

-nbp

No bias print False

-v

Version

-h

Shows this help message