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KMA(1) User Commands KMA(1)


kma - mapps raw reads to a template database


mapps raw reads to a template database.


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


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