Memory mapping and clarification of sequencing depth reccomendations

bhattlab / phanta

Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes

MIT License

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Open joshuakirsch opened 3 months ago

joshuakirsch commented 3 months ago

Hi folks,

Thanks for this great tool! Two things that I think would improve the tool/documentation:

Adding in kraken2 memory-mapping support. This would greatly speed up the tool.
Specifying whether the sequencing depth is in read pairs or total reads. In other words, are 50M PE reads (100M reads total) at the 50M level or the 100M level?

Thanks!

yipinto commented 3 months ago

Thank you! We will add memory-mapping support. The sequencing depth is in read pairs, so 10M reads means 10M pairs. Thanks for using Phanta!