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Unfortunately some bioinformatics tools require multiple passes over the FASTQ. Spades is an example of this.
by michaelbarton 4y ago
Unfortunately some bioinformatics tools require multiple passes over the FASTQ. Spades is an example of this.
- attractivechaos 4y agoFair enough. For the relatively few tools that don’t support streaming, you may generate temporary plain files in your pipeline. Spades itself is a pipeline and writes temporary files. It is anyway not realistic to expect wide adoption of zstd in the near future. If you want to save storage cost now, you have to take some trade off.