This Dentinger_readme20220405.txt file was generated on [20220405] by [Bryn T.M. Dentinger]
(Please update the file name to read AUTHOR_readmeYYYYMMDD.txt)
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GENERAL INFORMATION

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1. Title of Dataset 
Large Kraken2 database for Fungi

2. Author Information
  Principal Investigator Contact Information

        Name: Bryn T.M. Dentinger

           Institution: Natural History Museum of Utah & School of Biological Sciences, Unviersity of Utah

           Address: 301 Wakara Way, Salt Lake City, UT 84108

           Email: bdentinger@nhmu.utah.edu

  Associate or Co-investigator Contact Information

        Name:

           Institution:

           Address:

           Email:

  Alternate Contact Information

           Name:

           Institution:

           Address:

           Email:

3. Date of data collection (single date, range, approximate date) <suggested format YYYYMMDD>
20200329

4. Geographic location of data collection (where was data collected?): 
n/a

5. Information about funding sources that supported the collection of the data:
n/a

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SHARING/ACCESS INFORMATION

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1. Licenses/restrictions placed on the data:
CC BY NC – Allows others to use and share your data non-commercially and with attribution

2. Links to publications that cite or use the data:
Weinstein, S.B., W.Z. Stephens, R. Greenhalgh, J.L. Round, M.D. Dearing. Wild herbivorous mammals (genus Neotoma) host a diverse but transient assemblage of fungi. Symbiosis. In Revision.

3. Links to other publicly accessible locations of the data:

n/a

4. Links/relationships to ancillary data sets:

n/a

5. Was data derived from another source? yes

           If yes, list source(s):
The NCBI database is here: https://www.ncbi.nlm.nih.gov/genome/
The JGI database is here: https://mycocosm.jgi.doe.gov/mycocosm/home

6. Recommended citation for the data:

Dentinger, B.T.M. (2022). Large Kraken2 database for Fungi. The Hive: University of Utah Research Data Repository. https://doi.org/10.7278/S50d-154b-fppf 

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DATA & FILE OVERVIEW

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1. File List

   A. Filename: bigDB.tar.gz       

      Short description: kmer database formatted for Kraken2       


   B. Filename: AddTaxID_list.py       

      Short description: python script that will lookup NCBI TaxIDs based on scientific names to modify FASTA headers in JGI genomes so they can be added to the Kraken2 database; courtesy of Heath O'Brien       

   C. Filename:        

      Short description:

2. Relationship between files:        

AddTaxID_list.py was used to modify FASTA headers in JGI genomes to make them compatible with Kraken2


3. Additional related data collected that was not included in the current data package:

n/a


4. Are there multiple versions of the dataset? no

   If yes, list versions:

           Name of file that was updated:

                     i. Why was the file updated? 

                ii. When was the file updated?

           Name of file that was updated:

                      i. Why was the file updated?

                    ii. When was the file updated?

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METHODOLOGICAL INFORMATION

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1. Description of methods used for collection/generation of data: 

<Include links or references to publications or other documentation containing experimental design or protocols used in data collection>


The database was built using the following commands:

kraken2-build --download-taxonomy --db bigDB && \

kraken2-build --download-library archaea --db bigDB && \

kraken2-build --download-library bacteria --db bigDB && \

kraken2-build --download-library viral --db bigDB && \

kraken2-build --download-library plasmid --db bigDB && \

kraken2-build --download-library human --db bigDB && \

kraken2-build --download-library fungi --db bigDB && \

kraken2-build --download-library plant --db bigDB && \

kraken2-build --download-library protozoa --db bigDB && \

kraken2-build --download-library UniVec_Core --db bigDB && \

kraken2-build --download-library nt --db bigDB


#now you can add the JGI fungal genomes with FASTA headers modified to include NCBI TaxIDs

find jgi_genomes -name '*.fasta' -print0 | xargs -P -0 -I{} -n1 kraken2-build --add-to-library {} --db bigDB


2. Methods for processing the data: <describe how the submitted data were generated from the raw or collected data>


3. Instrument- or software-specific information needed to interpret the data:

Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0
The tar.gz file is a database formatted for use with the software Kraken2 (https://ccb.jhu.edu/software/kraken2/). The citation refers to the software.

4. Standards and calibration information, if appropriate:

5. Environmental/experimental conditions:

6. Describe any quality-assurance procedures performed on the data:

7. People involved with sample collection, processing, analysis and/or submission:

-----------------------------------------

DATA-SPECIFIC INFORMATION FOR: [FILENAME]

-----------------------------------------

<create sections for each dataset (or file if appropriate) included>

1. Number of variables:


2. Number of cases/rows: 


3. Variable List

    A. Name: [variable name]

       Description: [description of the variable]

                    Value labels if appropriate

    B. Name: [variable name]

       Description: [description of the variable]

                    Value labels if appropriate

4. Missing data codes:

        Code/symbol        Definition

        Code/symbol        Definition

5. Specialized formats of other abbreviations used