Script use to process LoopSeq full length 16S rRNA gene sequence data for the manuscript in revision: J.E. Hinkle, J.P. Chanton, M.A. Moynihan, S.E. Ruff, A. Teske, Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq).
Script used to process LoopSeq data using DADA2 and generate a phyloseq object. This script follows the DADA workflow) with modifications suggested for long-read sequencing and Loop Genomics. This workflow uses cutadapt to identify full-length 16S rRNA gene sequences. Reads without both primers are removed, as they are not considered full-length. However, note that it is possible to have relatively long sequence reads (e.g. 1200bp) that are not full-length and might still be useful for some analyses. As alternative to using cutadapt, sequences could be filtered by length.
Additionally, scripts used to assess Alpha and Beta diversity are included.