LFQC - Fastq compressor

This project contains the source code for the publication:

Marius Nicolae, Sudipta Pathak and Sanguthevar Rajasekaran, "LFQC: A lossless compression algorithm for FASTQ files"

http://bioinformatics.oxfordjournals.org/content/31/20/3276.abstract

The latest version can be found at:

https://github.com/mariusmni/lfqc

Prerequisites:

• Unix system with at least 4gb of RAM (preferably 8)
• Ruby

Change directory to lfqc/

To compress:

ruby lfqc.rb file.fastq  

Creates archive file.fastq.lfqc

ruby lfqc.rb -ls454 file.fastq
ruby lfqc.rb -solid file.fastq
ruby lfqc.rb -solexa file.fastq

Same as above but specifies type of dataset

To uncompress:

ruby lfqcd.rb file.fastq.lfqc

Uncompresses to file.fastq (dataset type does not matter)

ruby lfqcd.rb file.fastq.lfqc output.fastq 

Uncompresses to output.fastq

Compiling zpaq and lpaq (if errors occur)

Lfqc depends on two compression algorithms: zpaq702 and lpaq8. Their binaries are included in the project but they may not work on your system. Fortunately, their source code is also included so you can build them on your machine.

Please try to run the zpaq binary with no arguments. It should print usage. If it doesn't print usage, you have to delete the binary and run make in the zpaq folder. This should regenerate zpaq for your machine.

Similarly, try to run the lpaq8 binary. It should print usage options. If it doesn't, you have to delete the binary and run make. Lpaq is a bit old so it requires some 32 bit libraries. If your machine is 64 bit you may have to first install some 32 bit libraries. The following guide should help:

http://www.cyberciti.biz/tips/compile-32bit-application-using-gcc-64-bit-linux.html

If the above link is broken, a cached version of the page can be found here.

Note: If you get an error on decompression similar to

lfqcd.rb:29:in `join': no implicit conversion of nil into String (TypeError)

then most likely the lpaq8 or zpaq8 binary do not work on your machine. They should be recompiled, even if they do print usage!

Contact

For questions, suggestions, bugs please contact:

Marius Nicolae 
marius.nicolae (at) engr.uconn.edu