KMERRESISTANCE

NAME

kmerresistance - correlates mapped genes with the predicted species of WGS samples

SYNOPSIS

DESCRIPTION

KmerResistance correlates mapped genes with the predicted species of WGS samples, where this this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available.

OPTIONS

	-i		Input/query file name REQUIRED
	-o		Output file REQUIRED
	-t_db		Template DB REQUIRED
	-s_db		Species DB REQUIRED
	-id		ID threshhold 70.0
	-dct		Depth correction threshhold 0.1
	-kma		alternative KMA kma

KMA options:

	-i		Input/query file name None REQUIRED
	-o		Output file None REQUIRED
	-t_db		Template DB None REQUIRED
	-k		Kmersize 16
	-e		evalue 0.05

-delta

Align in pieces of delta 511

-mem_mode

Use kmers to choose best template, and save memory False

-ex_mode

Searh kmers exhaustively False

-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

	-mp		Minimum phred score 30
	-5p		Cut a constant number of nucleotides from the 5 prime. 0

-Sparse

Run KmerFinder False

	-ID		Minimum ID 1.0%
	-ss		Sparse sorting (q,c,d) q
	-shm		Use shared DB made by kma_shm 0 (lvl)
	-swap		Swap DB to disk 0 (lvl)
	-1t1		Skip HMM False
	-boot		Bootstrap sequence False
	-mrs		Minimum alignment score, normalized to alignment length 0.5

-reward

Score for match 1

-penalty

Penalty for mismatch -2

-gapopen

Penalty for gap opening -3

-gapextend

Penalty for gap extension -1

-h

Shows this help message

EXAMPLES

Mapping reads against resistance genes:

kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder -s_db bacteria

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.