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slimfastq would efficiently compresses/decompresses fastq files. It features:

  • High compression ratio
  • Relatively low CPU, memory usage
  • Truly lossless compression/decompression
  • Posix piping friendly (i.e. fastq input/output steam is serialzed during compression/decompression)


% slimfastq *file.fastq* *new-file.sfq* : compress *file.fastq* to *new-file.sfq* % slimfastq -1 *file.fastq* *new-file.sfq*: compress *file.fastq* to *new-file.sfq*, using little CPU/memory resources (-1 to -4 are levels of compression/resources trade-offs, -3 is default)

% slimfastq file.sfq : decompress file.sfq to stdout (format is determined by stamp, not name) % slimfastq file.sfq *file.fastq : decompress file.sfq to file.fastq

% slimfastq -h : get help

pipe usage: % gzip -dc file.fastq.gz | slimfastq -f file.sfq : convert from gzip to sfq format (and save a lot of disk space) % slimfastq file.sfq | md5sum - : get the checksum of the decompressed file without creating a file

The multi threads FAQ

The main reason slimfastq is a single thread application is to avoid the overhead of semaphores, L2 flushes, and context switches. The goal is to focus on the speed of N files compression/decompression instead of a single file. Use slimfastq.multi script (located under tools/) to compress/decompress multiple files in parallel. The '-h' argument, as expected, will provide help. This script can be easily edited for a sepcial setup. Please do not hesitate to email me if any help is needed.


Simple compilation:

  • run "make" or "make test" (If the compilation fails, please let me know).

Profile optimized compilation:

  • Compile slimfastq in a gcc profile generator mode (use 'make').
  • Compress/decompress some of your fastq files - this will generate some *.gcda files.
  • Recompile with optimization flags for the profiler generated data (use 'make slimfastq.opt'). (For whatever it's worth, the author of this page could not notice any significant performance change yield by the optimized compilation.)


"make test" will compress, decompress and compare all the fastq files in the ./samples dir. Some testing tips to check your own fastq files:

  1. slimfastq is a lossless compression and posix pipes friendly, therefore it's easy to check the integrity of a large file with checksums:
% md5sum large-file.fq % ./slimfastq largefile.fq -O /tmp/tst.sfq % ./slimfastq /tmp/tst.sfq | md5sum - (if md5sum don't match, one can use ./tools/ to the bad line. And I'll be grateful for a bug report) 2) use time. Example: % /usr/bin/time -f " IO : io=%I faults=%F\n MEM: max=%M kb Average=%K kb\n CPU: Percentage=%P real=%e sys=%S user=%U" slimfastq large-file.fq /tmp/a.tst -O 3) Performance wise, a single file compression/decompression is not very interesting. The script tools/slimfastq.multi can be used to evaluate performance of concurrent files compression/decompression. This script can be edited to use with other compression softwares - general or fastq specific. 4) Using slimfastq.multi, try to increase/decrease thread count to find the optimal number for a specific system.


After compile

  • run "sudo make install"
  • Alternatively to "make install", copy the "slimfastq" executable and the "tools/slimfastq.multi" script to any location.


The BSD 3-Clause


slimfastq was developed and optimized for x86_64 GNU/Linux and Darwin OS. For other system's support requests, please contact Josef Ezra.


Josef Ezra (jezra at, (jezra at