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#Using JDNA This tutorial explains how to use JDNA to compress DNA sequences based on a representative reference.

Basic usage

$ java -jar JDNA.jar <TASK> <REFERENCE> <INPUT> <OUTPUT>

arguments:

• TASK: The task to be executed (COMPRESS, or DECOMPRESS)
• REFERENCE: The path to the file containing the reference sequence
• INPUT: The path to the to-be-compressed or decompressed file
• OUTPUT: The path to the resulting (de)compressed file

examples:

$ java -jar JDNA.jar COMPRESS human_g1k_v37.fasta HG01390.fasta HG01390.cmp
$ java -jar JDNA.jar DECOMPRESS human_g1k_v37.fasta HG01390.cmp HG01390.fasta

A straightforward example

Download the JAR file:

$ wget  https://github.com/Camandros/jdna/raw/master/JDNA/JDNA.jar

Download two example files containing DNA sequences (1kB each):

$ wget https://raw.githubusercontent.com/Camandros/jdna/master/JDNA/ref_ex.raw
$ wget https://raw.githubusercontent.com/Camandros/jdna/master/JDNA/inp_ex.raw

Execute the JDNA to compress the input sequence:

$ java -jar JDNA.jar COMPRESS ref_ex.raw inp_ex.raw out_ex.cmp

Run the following du command to verify the size of the input and output files (in bytes using the -b option):

$ du -b inp_ex.raw out_ex.cmp
1032	inp_ex.raw
44  	out_ex.cmp

Execute the JDNA to decompress the output file:

$ java -jar JDNA.jar DECOMPRESS ref_ex.raw out_ex.cmp inp_ex_dcmp.raw

Run a checksum command (e.g., md5sum) to verify that the decompressed output is exactly the same as the original to-be-compressed input (JDNA is lossless):

$ md5sum inp_ex.raw inp_ex_dcmp.raw 
9217d97a92cf8d76a92ef60a9101f468  inp_ex.raw
9217d97a92cf8d76a92ef60a9101f468  inp_ex_dcmp.raw

Customizing JDNA

JDNA allows users to provide a configuration file (config.ini) in the same folder as the JAR file with customized values for the following parameters:

Parameter	Default Value	Description
kmer_size	20	Size of k-mer when indexing the reference (in bp)
search_window	120	Window size for brute-force searches (in bp)
index_window	200	Window size for indexed searches (in bp)
dcmp_mem	1	Maximum amount of memory to be used during decompression (in MB)
block_size	250	Size of each reference block to be loaded to the main memory (in MB)

example:

kmer_size=20
search_window=120 
index_window=200 
dcmp_mem=1 
block_size=250

Notes and throubleshooting

• JDNA accepts input files with two extensions: .raw and .fasta. The former is a raw DNA sequence that contains only A, C, G, T, and N nucleotides, while the latter accepts files with comment lines (i.e., lines started by the ">" character).