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.