I am starting this discussion to know a general view point about the annoying struggle of compressing and decompressing fastq file (as all the analysis in NGS starts with this file). While it is understood that compression is important in order to save space, there are a couple of routine problems I face where a considerable amount of time is wasted in either compressing or decompressing fastq files.
Now, for basic analysis like trimming, cleaning, taking the fastq stats, tools can be classified into below categories:
- tools which only work on compressed fastq files (.gz)
- tools which only work on decompressed fastq files
- tools which work on decompressed fastq files and themselves decompress files before analysing.
- tools which work on both compressed and decompressed files (e.g trimmomatic, fastqc)
Isn't it there is a need of unanimous protocol/guidelines to design tools which work on compressed fastq files?