table of contents
KMA(1) | User Commands | KMA(1) |
NAME¶
kma - mapps raw reads to a template database
DESCRIPTION¶
mapps raw reads to a template database.
OPTIONS¶
- -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
AUTHOR¶
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 |