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Publicly Hosted MetaScope Databases and Bowtie 2 Indices

Sean Lu

2025-01-30

Source: vignettes/vignette_docs/publicly_hosted_indices_and_accessions.Rmd
publicly_hosted_indices_and_accessions.Rmd

Introduction

To mitigate the effort of downloading reference genomes, taxonomy identifier databases, and constructing Bowtie 2 indices, we provide pre-compiled versions as described below. Current versions of all of these files can be constructed with MetaScope’s functions if users choose not to download the files here.

All databases are hosted centrally on a Box drive for download. A brief explanation of available files follows:

Taxonomy Annotation Database (2024_Accession_Taxa)

This file is a zip compressed folder containing a database of taxonomy information prepared with download_accessions() as part of MetaScope’s MetaRef module.

These files are required for MetaScope’s MetaID module and MetaBLAST module. (Note that MetaBLAST is an optional module).

It is highly recommended that all users download this database if they are using NCBI or SILVA databases. Otherwise, users will need to run MetaScope::download_accessions() to obtain this database.

BLASTn 16S Database (metascope_blast_indices/2024_blast_16S)

This folder contains BLASTn files for use with the MetaBLAST module. The MetaBLAST is an optional, yet highly recommended, component of the MetaScope workflow.

This folder contains the neccessary BLASTn indices to use BLASTn against the NCBI 16S ribosomal RNA database.

Note: The db_path argument for ‘metascope_blast()’ should included as follows:

metascope_blast(
  ..., # Necessary parameters here
  db_path = "/path/to/file/16SribosomalRNA" # Alter the db_path accordingly
)

MetaScope Bowtie2 Indices (metascope_bowtie2_indices)

Users of the MetaScope pipeline can easily and efficiently obtain reference genomes of interest using the download_refseq() function. However, the additional step of creating Bowtie 2 indices from these genomes to align them with sample data can add hours to these initial steps.

This folder contains various prebuilt bowtie2 indices that can be used with the the align_target_bowtie() and filter_host_bowtie functions. The user’s local path to these indices should be supplied to the lib_dir argument of those functions.

The following indices are available in Box drive:

  1. 2024_ncbi_16S The NCBI 16S ribosomal RNA database
  2. Greenegenes 13_8 The Greengenes 13.8 16S ribosomal RNA database
  3. MetaScope RefSeq 2023 The entire bacteria, fungi, homo_sapiens, human_T2T, mus_musculus, and viruses refseq nucleotide database downloaded via download_refseq() in 2023
  4. MetaScope RefSeq 2022 The entire bacteria, fungi, human, mouse, and viruses refseq nucleotide database downloaded via download_refseq() in 2022
  5. MetaScope RefSeq 2020 The entire bacteria, fungi, human/mouse, phix174, and viral refseq nucleotide database downloaded via download_refseq() in 2020
  6. PathoScope RefSeq 2018 The entire bacteria, mouse, and viral refseq nucleotide database downloaded via PathoScope 2.0 software in 2018
  7. PathoScope RefSeq 2015 The entire bacteria, fungi, human/mouse, phix174, and viral refseq nucleotide database downloaded via PathoScope 2.0 software in 2015
  8. SILVA 138.1 The SILVA 138.1 16S ribosomal RNA database