kma - maps and/or aligns raw reads to a template database
- 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
This manpage was written by Nilesh Patra for the Debian
distribution and can be used for any other usage of the program.