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Feature Request: support sralite format. #31

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slbai01 opened this issue Oct 21, 2023 · 1 comment
Open

Feature Request: support sralite format. #31

slbai01 opened this issue Oct 21, 2023 · 1 comment

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@slbai01
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slbai01 commented Oct 21, 2023

SRA data are available either with full base quality scores (SRA Normalized Format), or with simplified quality scores (SRA Lite), depending on user preference. Both formats can be streamed on demand to the same filetypes (fastq, sam, etc.), so they are both compatible with existing workflows and applications that expect quality scores. However, the SRA Lite format is much smaller, enabling a reduction in storage footprint and data transfer times, allowing dumps to complete faster. The SRA toolkit defaults to using the SRA Normalized Format that includes full, per-base quality scores, but users can opt to use simplified quality scores in their analysis by requesting the SRA Lite version to save time on their data transfers.

Can you please add download parameters to support the smaller and more concise sralite format?

@wwood
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wwood commented Dec 13, 2023

I like this idea, but haven't had the time just yet. WDYT about this being implemented as a --via-sralite flag so you can get the fastq file, as well as just having -m sralite?

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