Discrepancy in Read Counts in NextITS Analysis

[atfdh]

Hi,

I used the NextITS pipeline to analyze full-length ITS reads obtained through PacBio sequencing. However, I do not understand why the total number of reads in the OTU_table_LULU for each sample differs from the ITSx_Extracted_Reads shown in the run_summary results.

I appreciate any help you can provide!

[vmikk]

Hello @atfdh ,

It's normal for the number of reads to be lower in the final OTU table. The discrepancy arises because ITSx extraction occurs early in the processing pipeline. In later stages, NextITS removes short sequences, chimeras, tag-jump artifacts, and poor-quality singletons. These steps reduce the total number of reads, leading to fewer reads in the OTU table. For more details, please refer to the NextITS workflow scheme (https://next-its.github.io/#nextits-workflow).