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Yet Another 16S rRNA database

ya16sdb is a pipeline for downloading, curating, and annotating a database of bacterial 16S rRNA sequences. This repository also implements a web application (https://ya16sdb.labmed.uw.edu/) that can be used to visualize the distance-based relationships among sequences for a given species.

The purpose of the project is to provide a high quality source of bacterial 16S rRNA sequences that is up to date with NCBI, in a format that is useful as an input for various bioinformatics pipleines such as blast searching, phylogenetic reference set creation, sequence-based taxonomic assignment, etc.

Project information

This project is a product of ongoing research interests of Noah Hoffman (https://faculty.washington.edu/ngh2/home/pages/software.html) at the University of Washington in the Department of Laboratory Medicine.

Christopher Rosenthal is the primary author of the pipeline.

The pipeline heavily relies on taxtastic (https://github.com/fhcrc/taxtastic) and deenurp (https://github.com/fhcrc/deenurp), both of which began as collaborations with Erick Matsen at The Fred Hutchinson Cancer Research Center in Seattle, WA.

Please cite this project as

Rosenthal C and Hoffman NG. 2019. ya16sdb: a pipeline for creating a collection of high-quality bacterial 16S rRNA sequences from NCBI. Version 0.6.1. University of Washington. https://github.com/nhoffman/ya16sdb

Overview

At a high level, this pipeline does the following:

  • Downloads annotation for all available sequence records from the NCBI matching search terms for 16S rRNA.
  • Retrieves sequence records for corresponding full length (or near full-length) 16S rRNA genes; this involves extracting subsequences from genome sequences or contigs.
  • Ensures that all records are 16S rRNA genes
  • Ensures that sequences are in a consistent orientation.
  • Identifies the taxonomic lineage of each record.
  • Annotates records as a "type strain" (according to NCBI's definition of type strain), "published" (annotation has an accompanying PubMed ID), "refseq" (belonging to the Genbank refseq collection), or "direct" (direct submissions).
  • Discards records likely to be mis-annotated using deenurp filter-outliers.
  • Provides various subsets of annotated sequences. Each record subset provides sequence metadata, sequences, taxonomic lineages, and a blast database. For example:
    • only records with taxonomic name consistent with species-level classifications
    • type strains only
    • outliers removed
    • downsampled to a subset of sequences for each species, prioritizing type strains and "published" records.

Docker

Docker image can be built with the following:

docker build --tag ya16sdb:latest .

Once a Docker image has been built a Singularity image can be built using the docker daemon:

singularity build ya16sdb.img docker-daemon://ya16sdb:latest

A Singularity image can also be built using a Singularity Docker container:

docker run --volume /var/run/:/var/run/ --volume $(pwd):$(pwd) --workdir $(pwd) singularity:latest build ya16sdb.img docker-daemon://ya16sdb:latest

Pipeline execution

The virtual containers have a predefined entry point to the SConstruct pipeline file.

To execute using Docker just a settings.conf file is required and can be run as follows:

docker run --volume $(pwd):$(pwd) --workdir $(pwd) ya16sdb:latest

And with Singularity

singularity run --bind $(pwd) --pwd $(pwd) ya16sdb.img