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.
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
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 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
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