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fqzip is a Java command line program which compresses FASTQ files using the following methods:

  • BZIP2 for sequence data
  • PPM + Huffman for quality data
  • Efficient superblock encoding and BZIP compression for header data

FQZip uses a premade Huffman tree index for the PPM quality compression. For that, it must learn an existing FASTQ file for it to generate an efficient encoding. The premade PPM dictionary consists of multiple Huffman trees for every context - each context consists of the current sequence identifier (A/C/T/G) currently being encoded or decoded, the current position (between 0 and 100) and the last 2 quality and sequence characters encoded. When compressing and decompressing, the correct Huffman tree is chosen to decode the decoded output to the bitstream, and every symbol causes the context to change, so no two symbols actually belong to the same tree.

The header is also compressed with domain-specific compression, which uses super-blocks. Each block has its own fixed structure, and variable field types which are automatically identified and built per block. Then, only the needed information is stored, and compression is achieved by storing 0-bit information fields, such as incremental fields which increment all the way through the block, or low bit information fields which can be packed tightly.

Sequence is compressed using BZIP2 which is very efficient for sequence data, but should be eventually replaced by alignment compression.

Also, the compression and decompression of FASTQ files MUST be done using the same tree!

Another limitation of the current code is that it compresses code into separate files, depending on the number of threads used. Therefore, the same number of threads must be used to compress and decompress the data. The recommended amount of threads should be the number of processors your machine is using.

Currently, the tree is always created and read to the "tree.out" file.


To use fqzip, run it using a Command line interface.

Learning mode

Use a large FASTQ file with data which resembles the rest the data you wish to compress.

java -jar fqzip.jar learn <FASTQ FILE>

Compression mode

The compression is done to 3 files per thread using the output prefix.

java -jar fqzip.jar compress <FASTQ INPUT FILE> <OUTPUT PREFIX> <NUMBER OF THREADS>

Decompression mode

The decompression mode reads all the files it requires using the output prefix and the number of threads, and writes them out into a FASTQ file.

java -jar fqzip.jar decompress <INPUT PREFIX> <FASTQ OUTPUT FILE> <NUMBER OF THREADS>



java -jar fqzip.jar compress input.fastq output 4

Will generate the following files:


To decompress the FASTQ file back to the original, use:

java -jar fqzip.jar decompress output input-decompressed.fastq 4

About The Team

FQZip is an IDC (Interdisciplinary Center - Herzliya) project lead by Inbal Landsberg for the sequence squeeze competition. The creators of FQZip are Or Peled, Barak Yacov, Yonatan Amir, Dan Benjamin and Ron Reiter.

Sequence Squeeze -


The code is given under the BSD-3 License.