New Low Biomass Metagenomics Pipelines - AWG review needed

asaravia · February 12, 2026, 2:09pm

Hi @PPawg members (and also the @MicrobesAWG members if you believe you have the expertise to review-comment):

We have drafted two new pipelines for processing low biomass metagenomics datasets that are ready for your review. Please provide your feedback ASAP and no later than February 28th.

The Long-read (Nanopore) Low Biomass Metagenomics Pipeline is available here:

github.com/nasa/GeneLab_Data_Processing

Metagenomics/Low_Biomass/Nanopore/GL-DPPD-7116.md

DEV_Metagenomics_low_biomass

# Bioinformatics pipeline for Low biomass long-read metagenomics data

> **This document holds an overview and some example commands of how GeneLab processes low-biomass, long-read metagenomics datasets. Exact processing commands for specific datasets that have been released are provided with their processed data in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**  

---

**Date:** January MM, 2026  
**Revision:** -  
**Document Number:** GL-DPPD-7116  

**Submitted by:**  
Olabiyi A. Obayomi (GeneLab Analysis Team)  

**Approved by:**  
Samrawit Gebre (OSDR Project Manager)  
Jonathan Galazka (OSDR Project Scientist)  
Amanda Saravia-Butler (GeneLab Science Lead)  
Barbara Novak (GeneLab Data Processing Lead)

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The Short-read (Illumina) Low Biomass Metagenomics Pipeline is available here:

github.com/nasa/GeneLab_Data_Processing

Metagenomics/Low_Biomass/Illumina/GL-DPPD-7117.md

DEV_Metagenomics_low_biomass

# Bioinformatics pipeline for Low biomass short-read metagenomics data

> **This document holds an overview and some example commands of how GeneLab processes low-biomass, short-read metagenomics datasets. Exact processing commands for specific datasets that have been released are provided with their processed data in the [Open Science Data Repository (OSDR)](https://osdr.nasa.gov/bio/repo/).**  

---

**Date:** January MM, 2026  
**Revision:** -  
**Document Number:** GL-DPPD-7116  

**Submitted by:**  
Olabiyi A. Obayomi (GeneLab Analysis Team)  

**Approved by:**  
Samrawit Gebre (OSDR Project Manager)  
Jonathan Galazka (OSDR Project Scientist)  
Amanda Saravia-Butler (GeneLab Science Lead)  
Barbara Novak (GeneLab Data Processing Lead)

This file has been truncated. show original

@Alex @Haley_Sapers @gregcaporaso @lorna @Rettberg @jneufeld @barbara.novak @Stighe @stefan_green @gebresg @olabiyi @lguan @kjvvenkat @cdavis

ccnaney · February 12, 2026, 3:34pm

@asaravia Would it be okay if I use your markdown style and content (not copying, just components) as a template for my HTGAA 2026 homework?

tmn2126 · February 12, 2026, 4:04pm

For 1. Basecalling

Since version Dorado v1.0.0, fast5 files haven’t been supported. It would be good to remove all reference to them. Fast5 files need to be converted to pod5 files first with the pod5 tool: Tools — Pod5 File Format 0.1.21 documentation

This pipeline looks really great! Thank you so much for establishing this resource.

@asaravia @olabiyi @barbara.novak

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New Low Biomass Metagenomics Pipelines - AWG review needed

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