kmerresistance - correlates mapped genes with the predicted
species of WGS samples
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.
- -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
- -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
Mapping reads against resistance genes:
-
kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder
-s_db bacteria
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.