cryfa is a FASTA/FASTQ compression and encryption tool. It uses AES (Advanced Encryption Standard) for the purpose of encryption. cryfa can be applied to any FASTA or FASTQ file (DNA sequences, headers and quality-scores). Compacting 3 DNA bases into 1 char, it uses a fixed block size packing. Compared with general compression tools, it allows to decrease the file size by a factor of 3, without creating security problems such as those derived from CRIME or BREACH attacks.

INSTALL

Get cryfa and make the project, using:

git clone https://github.com/pratas/cryfa.git
cd cryfa
cmake .
make

RUN

If you want to run cryfa in stand-alone mode, use the following command:

./cryfa [OPTION]... -k [KEY_FILE] [-d] [IN_FILE] > [OUT_FILE]

For example, to compress:

./cryfa -k pass.txt in.fq > comp

and, to decompress:

./cryfa -k pass.txt -d comp > orig.fq

Options are described in the following section.

If you want to compare cryfa with other methods, set the parameters in run.sh bash script, then run it:

./run.sh

With this script, you can download the datasets, install the dependencies, install the compression and encryption tools, run these tools, and finally, print the results.

OPTIONS

To see the possible options, type:

./cryfa -h

which provides the following:

SYNOPSIS
      ./cryfa [OPTION]... -k [KEY_FILE] [-d] [IN_FILE] > [OUT_FILE]

SAMPLE
      Compress   & Encrypt:   ./cryfa -k pass.txt in.fq > comp     
      Decompress & Decrypt:   ./cryfa -k pass.txt -d comp > orig.fq

DESCRIPTION
      Compress and encrypt FASTA/FASTQ files.

      The KEY_FILE specifies a file including the password.

      -h,  --help
           usage guide

      -k [KEY_FILE],  --key [KEY_FILE]
           key file name -- MANDATORY

      -d,  --dec
           decompress & decrypt

      -v,  --verbose
           verbose mode (more information)

      -s,  --disable_shuffle
           disable input shuffling

      -t [NUMBER],  --thread [NUMBER]
           number of threads

cryfa uses standard input and ouput streams, hence, it can be directly integrated with pipelines.

CITE

Please cite the following, if you use cryfa:

• D. Pratas, M. Hosseini and A.J. Pinho, "Cryfa: a tool to compact and encrypt FASTA files," 11'th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB), Springer, June 2017.

RELEASES

• Release 2: FASTA and FASTQ handling.
• Release 1: FASTA handling.

ISSUES

Please let us know if there is any issues.

LICENSE

cryfa is under GPL v3 license. For more information, click here.