Provided by: kma_1.2.21-1_amd64
kma - mapps raw reads to a template database
mapps raw reads to a template database.
-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
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.