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KMA(1) User Commands KMA(1)

NAME

kma - mapps raw reads to a template database

DESCRIPTION

mapps raw reads to a template database.

OPTIONS

-o
Output file None REQUIRED
-t_db
Template DB None REQUIRED
-i
Input file name(s) STDIN
-ipe
Input paired end file name(s)
-int
Input interleaved file name(s)
-k
Kmersize DB defined
-e
evalue 0.05
-ConClave
ConClave version 1
-mem_mode
Use kmers to choose best template, and save memory False
-ex_mode
Searh kmers exhaustively False
-ef
Print additional features False
-vcf
Make vcf file, 2 to apply FT False/0
-deCon
Remove contamination False
-dense
Do not allow insertions in assembly False
-ref_fsa
Consensus sequnce will have "n" instead of gaps False
-matrix
Print assembly matrix False
-a
Print all best mappings False
-mp
Minimum phred score 30
-5p
Cut a constant number of nucleotides from the 5 prime. 0
-Sparse
Only count kmers False
-Mt1
Map only to "num" template. 0 / False
-ID
Minimum ID 1.0%
-ss
Sparse sorting (q,c,d) q
-pm
Pairing method (p,u,f) u
-fpm
Fine Pairing method (p,u,f) u
-apm
Sets both pm and fpm u
-shm
Use shared DB made by kma_shm 0 (lvl)
-swap
Swap DB to disk 0 (lvl)
-1t1
Skip HMM False
-ck
Count kmers instead of pseudo alignment False
-ca
Make circular alignments False
-boot
Bootstrap sequence False
-bc
Base calls should be significantly overrepresented. [True]
-bc90
Base calls should be both significantly overrepresented, and have 90% agreement. False
-bcNano
Call bases at suspicious deletions, made for nanopore. False
-and
Both mrs and p_value thresholds has to reached to in order to report a template hit. or
-mq
Minimum mapping quality 0
-mrs
Minimum alignment score, normalized to alignment length 0.50
-reward
Score for match 1
-penalty
Penalty for mismatch -2
-gapopen
Penalty for gap opening -3
-gapextend
Penalty for gap extension -1
-per
Reward for pairing reads 7
-cge
Set CGE penalties and rewards False
-t
Number of threads 1
-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 1.1.7