rambo-k - Read Assignment Method Based On K-mers
rambo-k [-h] -r REFFILE1 -R REFFILE2 [-n NAME1] [-N NAME2] -1 UNASSIGNED1 [-2 UNASSIGNED2] [-k KMERSIZES] [-o OUTPATH] [-a AMOUNT] [-t THREADS] [-x CHUNKSIZE] [-g GAPSIZE] [-c CUTOFF_LOWER] [-C CUTOFF_HIGHER] [-d] [-f FILETYPE]
RAMBO-K is a reference-based tool for rapid and sensitive extraction of one organisms reads from a mixed dataset. It is based on a Markov chain implementation, which uses genomic characteristics of each reference to assign reads to the associated set.
- -h, --help
- show this help message and exit
- -r REFFILE1, --reffile1 REFFILE1
- Reference file of species 1 in fasta-format. Should pair with name1
- -R REFFILE2, --reffile2 REFFILE2
- Reference file of species 2 in fasta-format. Should pair with name2
- -n NAME1, --name1 NAME1
- Name of species 1
- -N NAME2, --name2 NAME2
- Name of species 2
- -1 UNASSIGNED1, --unassigned1 UNASSIGNED1
- Fasta- or fastq-file containing mixed reads.
- -2 UNASSIGNED2, --unassigned2 UNASSIGNED2
- Fasta- or fastq-file containing mixed reads, only required in paired end mode.
- -k KMERSIZES, --kmersizes KMERSIZES
- Order of Markov-Chain/kmer length. Enter as range (e.g. 4:8) or list (e.g. 4,6,8) or integer (e.g. 8). Default = 8
- -o OUTPATH, --outpath OUTPATH
- Folder to write results to. Default = $name1_$name2/ in your working directory
- -a AMOUNT, --amount AMOUNT
- Number of reads to be simulated, default = 50000
- -t THREADS, --threads THREADS
- Number of Threads to use
- -x CHUNKSIZE, --chunksize CHUNKSIZE
- Size of chunks created at a time for simulation, default = 100000. Only change if you know what you are doing!
- -g GAPSIZE, --gapsize GAPSIZE
- Estimated size of gapsize in case of paired end reads, default = 1
- -c CUTOFF_LOWER, --cutoff_lower CUTOFF_LOWER
- Lower cutoff: Output only reads with a score lower than or equal to this value, use m1 for -1
- -C CUTOFF_HIGHER, --cutoff_higher CUTOFF_HIGHER
- Higher cutoff: Output only reads with a score higher than or equal to this value, use m1 for -1
- -d, --delete_temp
- \Delete temporary files. Calculations will start from beginning next time.
- -f FILETYPE, --filetype FILETYPE
- Type of your input reads. fasta or fastq, default = fastq
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
|November 2016||rambo-k 1.21|