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RAMBO-K(1) User Commands RAMBO-K(1)

NAME

rambo-k - Read Assignment Method Based On K-mers

SYNOPSIS

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]

DESCRIPTION

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.

OPTIONS

show this help message and exit
Reference file of species 1 in fasta-format. Should pair with name1
Reference file of species 2 in fasta-format. Should pair with name2
Name of species 1
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.
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
Folder to write results to. Default = $name1_$name2/ in your working directory
Number of reads to be simulated, default = 50000
Number of Threads to use
Size of chunks created at a time for simulation, default = 100000. Only change if you know what you are doing!
Estimated size of gapsize in case of paired end reads, default = 1
Lower cutoff: Output only reads with a score lower than or equal to this value, use m1 for -1
Higher cutoff: Output only reads with a score higher than or equal to this value, use m1 for -1
\Delete temporary files. Calculations will start from beginning next time.
Type of your input reads. fasta or fastq, default = fastq

AUTHOR

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