---
name: "rambo-k"
section: "1"
platform: "linux"
package: "rambo-k"
version: "1.21+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/rambo-k"
---

# rambo-k(1)

Read Assignment Method Based On K-mers

## 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.