New Version 3.0

Shoreline Biome’s unique microbiome kits are the key to generating long-read next-generation sequencing data necessary to discriminate microbial strains from any sample. The SBanalyzer software enables discovery of never before detected species and strains from microbiome samples.  In addition, SBanalyzer simplifies taxonomic assignment from the Shoreline Biome full length 16S (V1-V9) or 16S-ITS-23S (StrainID) long amplicon kits using the proprietary Athena database built from curated contiguous 16S-ITS-23S sequences. Shoreline Biome’s ‘Expert User Protocol’  details the exact steps needed in conjunction with DADA2  for ASV inference/database-independent identification and tracking of novel sequences or strains within and across experiments. Together, these are the Shoreline Complete solution.


  • Fast and easy to use point-and-click interface
  • Easily run on a laptop or a CentOS command line
  • Automated demultiplexing of V1-V9 or 16S-ITS-23S (StrainID) long-read output
  • Accurate read mapping to proprietary Athena or SILVA Datavase
  • Categorization of both known and novel strains
  • Simple excel based and FASTQ file data outputs for comparing microbe taxa
  • Straight forward read extraction of interesting taxomnomies
  • Expert User protocol with R-script enables ASV assignment using DADA2 

Version 3.0 Highlights

  • Advanced classification for reads with poor homology to known ITS regions
  • Improved classification of unknowns by scanning for related genomes
  • Significantly faster processing speed
  • Greater read alignment and palindrome removal
  • Expanded Athena database: ~20K genomes & 66K 16S-ITS-23S regions
  • Updated SILVA v138 update included
  • Enables  the use of the downstream informatics tools DADA2, QIIME 2

On-demand webinar

Identification and Classification of Novel Bacterial Strains

Identification and classification of novel bacterial strains in microbiome samples enables a new level of resolution and discovery. Watch our free on-demand webinar to learn how The Shoreline Complete StrainID™, SBanalyzer™ software, and Athena™ database in conjunction with a bioinformatics pipeline featuring DADA2, identifies ASVs and classifies novel strains.


SBanalyzer Quick Start Guide

The SBanalyzer is set up to be a point and click software, and this video is a quick start guide on how to use the software to analyze results of a sequencing run. Click here to access the guide. 






  • Taxonomic classification and read quantification of microbes within samples
  • Excel-compatible output for sample to sample comparisons
  • Untrimmed and primer-trimmed FASTQ/FASTA demultiplexing options

Fast. Easy. Complete.

Ensure that no microbe is left behind with Shoreline SBanalyzer software. For more information, contact us.


Pre-print: Tracking Enteric Bacteria in Premature Infants

ASV fingerprints from longitudinal microbiome samples of twins from different NICUs were analyzed using StrainID and DADA2 and demonstrated the potential to track the source and spread of both commensals and pathogens. Please click the button below to read the full article. 


V1-V9 and Strain ID Kits

Shop Shoreline Biome kits for use with SBanalyzer version 3.0


Software/Hardware Requirements

  • SBanalyzer software* installation on Microsoft Windows 10 or Linux CentOS 7 or 8 

  • 1TB disk drive (2 TB recommended)

  • 32 GB RAM (64 for multiple simultaneous Sequel2 run analysis)

  • Processor Options: Six core i7 4 GHz minimum.

  • Microsoft Excel for Windows 10, Centos 8 GUI with LibreOffice

  • Can be run on Oracle VM with Centos 8 installed on Mac or Windows

  • Server with 32-core head node, 64GB RAM, 2TB hard drive is even better

    *Software license required


  1. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23. PMID: 27214047; PMCID: PMC492737
  2. DADA2
  3. QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed –
  4. SILVA rRNA database –
  5. CentOS