#JDNA JDNA is an implementation of the On-Demand Indexing algorithm for referential compression of aligned DNA sequences proposed in this paper. Note that the reference must always be in raw format (no endlines or comments, only base-pairs). I recommend using references consisting only of A,C,T,G or N, since compression is made to deal only with these bps.

#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.raw HG01390.fasta HG01390.cmp
$ java -jar JDNA.jar DECOMPRESS human_g1k_v37.raw 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).
• If the file is a .fasta then a .ccom file is generated. The .ccom file has the comments present in the FASTA file and the line numbers of those comments. For decompression, the compressed cmp file is assigned as input. JDNA will then search for a .ccom file with the same name as the cmp file. If the .ccom file is found then a .fasta file is generated.

Example (note that the file name is always HG01390):

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