is LSA compatible with drastically different seqeuncing depths per sample?

[jvollme]

I have a methodical question about your LSA pipeline:
I have four datasets obtained from the same habitat & sampling location on different years. These have been created using different Illumina plattforms producing different output yields and read lengths:

1.) Illumina Hiseq with ~170mio reads, ~120 bp each
2.) Illumina Miseq with ~50mio reads, ~220bp each
3+4.) Illumina Nextseq with 100-120mio reads per sample ~140 bp each

Are these divergences in the sequencing datasets compatible with your pipeline, or will your pipeline assume roughly equal sequencing depths for all samples?