Scroll to navigation

KMERRESISTANCE(1) User Commands KMERRESISTANCE(1)

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

Input/query file name REQUIRED
Output file REQUIRED
Template DB REQUIRED
Species DB REQUIRED
ID threshhold 70.0
Depth correction threshhold 0.1
alternative KMA kma

KMA options:

Input/query file name None REQUIRED
Output file None REQUIRED
Template DB None REQUIRED
Kmersize 16
evalue 0.05
Align in pieces of delta 511
Use kmers to choose best template, and save memory False
Searh kmers exhaustively False
Remove contamination False
Do not allow insertions in assembly False
Consensus sequnce will have "n" instead of gaps False
Print assembly matrix False
Minimum phred score 30
-5p
Cut a constant number of nucleotides from the 5 prime. 0
Run KmerFinder False
Minimum ID 1.0%
Sparse sorting (q,c,d) q
Use shared DB made by kma_shm 0 (lvl)
Swap DB to disk 0 (lvl)
-1t1
Skip HMM False
Bootstrap sequence False
Minimum alignment score, normalized to alignment length 0.5
Score for match 1
Penalty for mismatch -2
Penalty for gap opening -3
Penalty for gap extension -1
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.

June 2018 kmerresistance 2.0+git20180205.26467e9