kma(1)
maps and/or aligns raw reads to a template database
Description
KMA
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:
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-i |
Single end input(s) stdin |
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-ipe |
Paired end input(s) |
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-int |
Interleaved input(s) |
Output:
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-o |
Output prefix |
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-ef |
Output additional features False |
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-vcf |
Output vcf file, 2 to apply FT False |
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-sam |
Output sam, 4/2096 for mapped/aligned False |
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-nc |
No consensus file False |
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-nc |
No aln file False |
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-nf |
No frag file False |
-matrix
Output assembly matrix False
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-a |
Output all template mappings False |
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-and |
Use both mrs and p-value on consensus or |
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-oa |
Use neither mrs or p-value on consensus False |
Consensus:
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-bc |
Minimum support to call bases 0 |
-bcNano
Altered indel calling for ONT data False
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-bcd |
Minimum depth to cal bases 1 |
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-bcg |
Maintain insignificant gaps False |
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-ID |
Minimum consensus ID 1.0% |
-dense
Skip insertion in consensus False
-ref_fsa
Use n’s on indels False
General:
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-t_db |
Template DB |
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-p |
P-value 0.05 |
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-shm |
Use DB in shared memory 0 |
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-mmap |
Memory map *.comp.b False |
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-tmp |
Set directory for temporary files |
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-t |
Number of threads 1 |
-status
Extra status False
-verbose
Extra verbose False
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-c |
Citation |
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-v |
Version |
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-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
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-ss |
Sparse sorting (q,c,d) q |
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-Mt1 |
Map everything to one template False/0 |
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-pm |
Pairing method (p,u,f) u |
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-1t1 |
One query to one template False |
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-hmm |
Use a HMM to assign template(s) True |
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-ck |
Count k-mers over pseudo alignment False |
Chaining:
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-k |
K-mersize DB defined |
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-ts |
Trim front of seeds 0 |
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-ssa |
Seeds soround alignments False |
-ex_mode
Searh kmers exhaustively False
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-fpm |
Pairing method (p,u,f) u |
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-mq |
Minimum mapping quality 0 |
Alignment:
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-ca |
Circular alignments False |
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-mrs |
Minimum relative alignment score 0.5 |
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-mrc |
Minimum query coverage 0.0 |
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-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
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-per |
Reward for pairing reads 7 |
-Npenalty
Penalty matching N 0
-transition
Penalty for transition 2
-transversion
Penalty for transversion 2
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-sasm |
Skip alignment False |
Trimming:
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-mp |
Minimum phred score 20 |
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-eq |
Minimum avg. quality score 0 |
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-5p |
Trim 5 prime 0 |
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-3p |
Trim 3 prime 0 |
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-ml |
Minimum length 16 |
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-xl |
Maximum length on se 2147483647 |
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-boot |
Bootstrap sub-sequence False |
Presets:
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-apm |
Sets both pm and fpm u |
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-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.