NAME
kma - maps and/or aligns raw reads to a template database
DESCRIPTION
-
KMA-1.3.23 maps and/or aligns raw reads to a template database.
- Options:
-
Desc: Default:
-
Input:
- -i
-
Single end input(s) stdin
- -ipe
-
Paired end input(s)
- -int
-
Interleaved input(s)
-
Output:
- -o
-
Output prefix
- -ef
-
Output additional features False
- -vcf
-
Output vcf file, 2 to apply FT False
- -sam
-
Output sam, 4/2096 for mapped/aligned False
- -nc
-
No consensus file False
- -nc
-
No aln file False
- -nf
-
No frag file False
- -matrix
-
Output assembly matrix False
- -a
-
Output all template mappings False
- -and
-
Use both mrs and p-value on consensus or
- -oa
-
Use neither mrs or p-value on consensus False
-
Consensus:
- -bc
-
Minimum support to call bases 0
- -bcNano
-
Altered indel calling for ONT data False
- -bcd
-
Minimum depth to cal bases 1
- -bcg
-
Maintain insignificant gaps False
- -ID
-
Minimum consensus ID 1.0%
- -dense
-
Skip insertion in consensus False
- -ref_fsa
-
Use n's on indels False
-
General:
- -t_db
-
Template DB
- -p
-
P-value 0.05
- -shm
-
Use DB in shared memory 0
- -mmap
-
Memory map *.comp.b False
- -tmp
-
Set directory for temporary files
- -t
-
Number of threads 1
- -status
-
Extra status False
- -verbose
-
Extra verbose False
- -c
-
Citation
- -v
-
Version
- -h
-
Shows this help message
-
Template mapping:
- -ConClave
-
ConClave version 1
- -mem_mode
-
Base ConClave on template mappings False
- -proxi
-
Proximity scoring (negative for soft) False/1.0
- -ex_mode
-
Searh kmers exhaustively False
- -deCon
-
Remove contamination False
- -Sparse
-
Only count kmers False
- -ss
-
Sparse sorting (q,c,d) q
- -Mt1
-
Map everything to one template False/0
- -pm
-
Pairing method (p,u,f) u
- -1t1
-
One query to one template False
- -hmm
-
Use a HMM to assign template(s) True
- -ck
-
Count k-mers over pseudo alignment False
-
Chaining:
- -k
-
K-mersize DB defined
- -ts
-
Trim front of seeds 0
- -ssa
-
Seeds soround alignments False
- -ex_mode
-
Searh kmers exhaustively False
- -fpm
-
Pairing method (p,u,f) u
- -mq
-
Minimum mapping quality 0
-
Alignment:
- -ca
-
Circular alignments False
- -mrs
-
Minimum relative alignment score 0.5
- -mrc
-
Minimum query coverage 0.0
- -ml
-
Minimum alignment length 16
- -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
- -Npenalty
-
Penalty matching N 0
- -transition
-
Penalty for transition 2
- -transversion
-
Penalty for transversion 2
- -sasm
-
Skip alignment False
-
Trimming:
- -mp
-
Minimum phred score 20
- -eq
-
Minimum avg. quality score 0
- -5p
-
Trim 5 prime 0
- -3p
-
Trim 3 prime 0
- -ml
-
Minimum length 16
- -xl
-
Maximum length on se 2147483647
- -boot
-
Bootstrap sub-sequence False
-
Presets:
- -apm
-
Sets both pm and fpm u
- -cge
-
Set CGE penalties and rewards False
- -mint2
-
Set 2ng gen Mintyper preset False
- -mint3
-
Set 3rd gen Mintyper preset False
AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.