A program to re-arrange FASTQ file (.fastq.gz) reads in order to compress the file to a smaller size.

Just point squish at your input fastq.gz file, and supply it with the filename of the desired output file.

$ ./squish data/test1.fastq.gz output.gz
2023/11/01 19:18:05 Input file data/test1.fastq.gz of size 4481 Bytes
2023/11/01 19:18:05 3276 reads loaded
2023/11/01 19:18:05 3276 reads sorted
2023/11/01 19:18:05 Output file created output.gz of size 4045 Bytes
2023/11/01 19:18:05 Size reduced by 436 Bytes (0.0973)

The current implementation of squish loads all fastq reads into memory, so you will need available system memory equal to the uncompressed size, plus extra for overhead. Hopefully future versions of squish can reduce memory requirements.

Tests with various .fastq.gz files saw compression improvements ranging from 3-35%.

You can download a pre-built binary from the Releases page here.

You can build it from source with Go version 1.20+

go build -o ./squish ./main.go

(Makefile recipe for building is also included)