Repositories list

• tourmaline

  Public
  Amplicon sequence processing workflow using QIIME 2 and Snakemake

  noaa-omics-softwaresnakemakedada2+ 2debluramplicon-sequence-variants

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •20•45•45•0•Updated Feb 14, 2025Feb 14, 2025

• node

  Public
  TypeScript

  •0•1•2•0•Updated Feb 14, 2025Feb 14, 2025

• protocols

  Public
  Protocols used by AOML Omics labs, following the BeBOP-OBON standard

  noaa-omics-protocol

  Shell

  •

  Creative Commons Zero v1.0 Universal

  •2•1•7•0•Updated Feb 12, 2025Feb 12, 2025

• protocol_extract_dna_sedtrap_powersoil

  Public
  Protocol for extracting DNA from sediment trap samples using the Qiagen PowerSoil Pro Kit

  noaa-omics-protocol

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• protocol_pcr_ssu18sv9_emp

  Public
  Protocol for preparing 18S V9 (EMP) libraries for Michigan State RTSF

  noaa-omics-protocol

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• protocol_pcr_ssu16sv4v5_emp

  Public
  Protocol for preparing 16S V4-V5 (EMP) libraries for Michigan State RTSF

  noaa-omics-protocol

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• protocol_pcr_ssu12sv5v6_mifish

  Public
  Protocol for preparing 12S V5-V6 (MiFish) libraries for Michigan State RTSF

  noaa-omics-protocol

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• protocol_sampling_sterivex_dry

  Public
  Protocol for sampling water using Sterivex with no ZR beads or preservative (dry)

  noaa-omics-protocol

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• protocol_sampling_sterivex_beads

  Public
  Protocol for sampling water using Sterivex with Zymo ZR beads and DNA/RNA Shield

  noaa-omics-protocol

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• protocol_libprep_metag_illumina

  Public
  Protocol for preparing metagenomic libraries using Illumina DNA Prep

  noaa-omics-protocol

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• protocol_extract_dna_sterivex_kingfisher

  Public
  Protocol for extraction of DNA from Sterivex filters using a KingFisher robot (BeBOP format)

  noaa-omics-protocol

  0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• okex

  Public
  R

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

• biogoship

  Public
  R

  •0•0•4•0•Updated Jan 28, 2025Jan 28, 2025

• gfisher

  Public
  R

  •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

• gomecc

  Public
  Input files and data analysis for NOAA GOMECC-4 DNA project.

  noaa-omics-study

  HTML

  •1•0•0•0•Updated Jan 18, 2025Jan 18, 2025

• mitohelper

  Public
  Mitohelper: a mitochondrial reference sequence analysis tool for fish eDNA studies

  ednanoaa-omics-softwaremitofish+ 2mifishfish-edna-studies

  Python

  •9•18•0•0•Updated Jan 14, 2025Jan 14, 2025

• seusmbon

  Public
  Jupyter Notebook

  •0•0•17•0•Updated Sep 18, 2024Sep 18, 2024

• labelmaker

  Public
  Printable QR labels for samples

  noaa-omics-softwaretexlabelmaker+ 1label-sheet

  Python

  •

  Other

  •9•7•1•0•Updated Sep 2, 2024Sep 2, 2024

• sase

  Public
  C++

  •

  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated May 8, 2024May 8, 2024

• tutorials

  Public
  Tutorials for data science and bioinformatics

  noaa-omics-education

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •5•11•1•0•Updated May 3, 2024May 3, 2024

• edna2obis

  Public
  Code to convert eDNA metabarcoding data to Darwin Core for OBIS

  noaa-omics-softwarenoaa-omics-data

  Jupyter Notebook

  •

  MIT License

  •2•6•4•0•Updated Apr 29, 2024Apr 29, 2024

• amethyst

  Public
  Metagenomics analysis workflow

  Python

  •4•1•1•0•Updated Mar 11, 2024Mar 11, 2024

• omics-data-management

  Public
  Previous guide to omics data management, including NOAA Omics Data Management Plan.

  noaa-datanoaa-omics-data

  GNU General Public License v3.0

  •1•7•3•0•Updated Jan 12, 2024Jan 12, 2024

• datasets

  Public
  List of datasets generated by the AOML 'Omics program

  noaa-omics-data

  HTML

  •0•1•0•0•Updated Jan 9, 2024Jan 9, 2024

• sedtrap

  Public
  Files associated with the USGS GoM Sediment Trap (GMT cruises)

  noaa-omics-study

  R

  •0•2•3•0•Updated Sep 7, 2023Sep 7, 2023

• study-template

  Public template
  Create a new repository for each study using this template.

  noaa-omics-study

  R

  •0•0•1•0•Updated Aug 18, 2023Aug 18, 2023

• cloud-classroom

  Public
  Guides for using commercial cloud resources

  2•1•1•0•Updated Aug 1, 2023Aug 1, 2023

• sterivex

  Public
  Methods development for high-throughput eDNA sampling and extraction with Sterivex filters

  noaa-omics-study

  Jupyter Notebook

  •2•0•0•0•Updated Sep 28, 2021Sep 28, 2021

• erie

  Public
  Study of cyanobacterial harmful algal blooms in Lake Erie using autonomous sampling and DNA sequencing

  metagenomicsamplicon-sequencingnoaa-omics-study

  HTML

  •1•1•0•0•Updated Jul 1, 2021Jul 1, 2021

• roboboogie

  Public
  Protocols and labware specifications for the KingFisher Flex and Opentrons OT-2 robots

  kingfisheropentronsnoaa-omics-software

  Python

  •1•0•0•0•Updated Jun 1, 2021Jun 1, 2021