bionic (1) rambo-k.1.gz

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

       -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

AUTHOR

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