CHLA recommendation for ALAPY Compressor

File Size163.40 KB
Create DateJune 14, 2017

In March 2017, our laboratory collaborated with ALAPY company on our fastq files compression.
There were several requirements for fastq compression in our lab:
1. High compression ratio
2. Lossless compression
3. Zero tolerance to data corruption
4. Ability to use compressed fastq files in our NGS pipelines
5. Ability to decompress data back using our own resources at any time in the future for free
6. Free compression and decompression version of the tool for academia
7. Positive reviews from other bioinformatics professionals
8. High production level stability of the tool for integration into our pipelines
We selected ALAPY Compressor because it was the best match for our requirements.
In this collaboration with ALAPY we compressed over 2500 fastq.gz files in one week. This saved us 57% of storage space on our server. For quality control purposes all files were compressed, then decompressed and MD5 sums were compared with the original files. MD5 sums were matching exactly for 100% of files and that process was logged for future references. This made us comfortable to switch completely from gzip to ALAPY Compressor for our NGS work and delete original fastq.gz files. We are planning to use ALAPY Compressor in coming years.
We recommend ALAPY Compressor and collaborations with ALAPY on NGS-related projects.