rambo-k1

Usage

Overview

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