Can I run output from Illumina genome Analyser II, IIx and Illumina Hiseq 2000 with MetaPhlAn and HUMAnN and compare the output?

Hi there- @franzosa @fbeghini @Kelsey_Thompson

I have a dataset where some of the samples has been sequenced with Illumina Genome Analyser II, some with Illumina Genome Analyser IIx and the rest with Illumina Hiseq 2000. Now, I know that, I can run sequences from Genome analyser II and Hiseq 2000 with MetaPhlAn and HUMAnN, but not sure about the output from Genome analyser IIx. Can I run MetaPhlAn and HUMAnN with the sequence coming from Illumina Genome Analyser IIx platform?

Also, should I compare the relative abundances of the features (taxa and pathways) coming from Genome Analyser IIx Vs Hiseq2000 to find out differentially abundant taxa?
I mean, I am confused if it is suitable to compare sequences coming from different platforms.


  • It is definitely fair (and potentially interesting!) to compare the predicted composition of a biosample sequenced by different methods.

  • My understanding of the IIx platform is that it’s tuned for shorter reads, e.g. 2x 35 bp? MetaPhlAn 3 prefers to filter reads < 70 bp, so you might need to change that filter for use with the IIx platform (if you’re generating very short reads). HUMAnN is fine with a range of short read lengths (but needs special configuration for use with very long reads).