repaq is an open source tool for FASTQ compression: https://github.com/OpenGene/repaq
It repacks Illumina format FASTQ to a smaller binary file (.rfq), which can be further compressed by xz or pxz (.rfq.xz).
For NovaSeq data, the .rfq file can be much smaller than .fq.gz, and the compressing time is usually less than 1/5 of gzip compression.
The biggest advantage is that the .rfq file can be further compressed with xz, which is based on LZMA algorithm. The .rfq.xz file can be as small as 5% of the original FASTQ file, or smaller than 30% of the .fq.gz file. Note that usually the gz files are not compressible by xz.
This tool also supports non-Illumina format FASTQ (i.e. the BGI-SEQ format), but the compression ratio is not as good Illumina format FASTQ.
WARNING: be careful about using repaq for production before v1.0 is released, since its spec v1.0 has not been frozen.
take a look of the compression ratio
Here we demonstrate the compression ratio of two paired-end NovaSeq data. You can download these files and test locally.
nova.R1.fq: 1704 MB, the original read1 file,
nova.R2.fq: 1704 MB, the original read2 file,
nova.R1.fq.gz: 308 MB (CR 18.08%), the gzipped read1,
nova.R2.fq.gz: 325 MB (CR 19.07%), the gzipped read2,
nova.rfq: 333 MB (CR 9.77%), the repacked file of read1+read2,
nova.rfq.xz: 134 MB (CR 3.93%), the xz compressed
See? The size of final
nova.rfq.xz is only 3.39% of the original FASTQ files! You can decompress it and check the md5 to see whether they are identical!
Typically with one single CPU core, it takes less than 1 minute to convert
nova.R1.fq + nova.R2.fq to
nova.rfq, and takes less than 5 minutes to compress the
nova.rfq.xz by xz.
This binary is only for Linux systems: http://opengene.org/repaq/repaq
# this binary was compiled on CentOS, and tested on CentOS/Ubuntu
chmod a+x ./repaq
or compile from source
# get source (you can also use browser to download from master or releases)
git clone https://github.com/OpenGene/repaq.git
sudo make install
For single-end mode:
repaq -c -i in.fq -o out.rfq
repaq -d -i in.rfq -o out.fq
For paired-end mode:
repaq -c -i in.R1.fq -I in.R2.fq -o out.rfq
repaq -d -i in.rfq -o out.R1.fq -O out.R2.fq
-I always denote the first and second input files, while
-O always denote the first and second output files.
- the FASTQ input/output files can be gzipped if their names are ended
for paired-end data. the .rfq file created in paired-end mode is usually much smaller than the sum of the .rfq files created in single-end mode for R1 and R2 respectively. To obtain high compression rate, please always use PE mode for PE data.
compress .rfq to .rfq.xz with xz
To get highest compression ratio (need at least 16G RAM):
xz --lzma2="dict=1000000000" in.rfq
To get normal ratio (need at least 1G RAM):
xz -9 in.rfq
The latest version of xz supports multithreading, so you can specify the thread number with
xz -T4 -9 in.rfq
You can also use pxz for parallel xz compressing:
pxz -9 in.rfq
- lower compression ratio than
-9 is not recommended, since it will
not be faster. The difference is the RAM requirement.
STDIN and STDOUT
repaq can read the input from STDIN, and write the output to STDOUT.
--stdin if you want to read the STDIN for compression or
--stdout if you want to output to the STDOUT for
compression or decompression.
- in decompression mode, if
--stdout is specified, the output will be
interleaved PE stream.
- if the STDIN is an interleaved paired-end stream, specify
--interleaved_in to indicate that.
Here gives you an example of compressing the interleaved PE output from fastp by directly using pipes:
fastp -i R1.fq -I R2.fq --stdout | repaq -c --interleaved_in --stdin --stdout | xz -z -c > out.rfq.xz
FASTQ Format compatibility
repaq was initially designed for compressing Illumina data, but it also works with data from other platforms, like BGI-Seq. To work with repaq, the FASTQ format should meet following condidtions:
- only has bases A/T/C/G/N.
- each FASTQ record has, and only has four lines (name, sequence,
- the name and strand line cannot be longer than 255 bytes.
- the number of different quality characters cannot be more than 127.
repaq works best for Illumina data directly output by
-i, --in1 input file name (string [=])
-o, --out1 output file name (string [=])
-I, --in2 read2 input file name when encoding paired-end FASTQ files (string [=])
-O, --out2 read2 output file name when decoding to paired-end FASTQ files (string [=])
-c, --compress compress input to output
-d, --decompress decompress input to output
-k, --chunk the chunk size (kilo bases) for encoding, default 1000=1000kb. (int [=1000])
--stdin input from STDIN. If the STDIN is interleaved paired-end FASTQ, please also add --interleaved_in.
--stdout write to STDOUT. When decompressing PE data, this option will result in interleaved FASTQ output for paired-end input. Disabled by defaut.
--interleaved_in indicate that <in1> is an interleaved paired-end FASTQ which contains both read1 and read2. Disabled by defaut.
# following options are used to check the consistency of the compressed data
-p, --compare compare the files read by read to check the compression consistency. <rfq_to_compare> should be specified in this mode.
-r, --rfq_to_compare the RFQ file to be compared with the input. This option is only used in compare mode. (string [=])
-j, --json_compare_result the file to store the comparison result. This is optional since the result is also printed on STDOUT. (string [=])
-?, --help print this message