PRJNA860062 Assigned Taxonomy and QIIME2 Pipeline

PRJNA860062 Assigned Taxonomy:

This upload comprises two datasets with the assigned taxonomy for sequence variants of BioProject PRNJA860062.

PRJNA860062_ASVCounts_NCBItaxonomy.txt

PRJNA860062_ASVCounts_SILVAtaxonomy.txt

BioProject PRNJN860062 compares bacterial profiles of zebrafish larvae microbiota resulting from two different microbial colonization methods. The full description and sequence data for this project can be obtained from the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/bioproject). 

The dataset with the SILVA taxonomy can directly be obtained using the QIIME2 script included in this upload ('PRJNA860062_QIIME2Script.txt'). As previously noted by Lesack and Birol (2018), SILVA species annotations include nomenclature errors (DOI: 10.1101/441576). Therefore, the dataset with the NCBI taxonomy comprises a manually corrected taxonomy for BioProject PRNJA860062, based on the family to phylum level nomenclature of the NCBI taxonomy browser (https://www.ncbi.nlm.nih.gov/taxonomy).

Both files are tab-delimited text files, include the domain to species level taxonomy in the first 7 columns, and include the number of assigned sequence variants (ASVs) per taxon in the final 6 colums, corresponding to BioSample SAMN29820940, SAMN29820941, SAMN29820942, SAMN29820943, SAMN29820944, and SAMN29820945.

QIIME 2 Pipeline:

The QIIME2 script that was used to obtain the assigned SILVA taxonomy BioProject PRNJA860062 is uploaded as:

PRJNA860062_QIIME2Script.txt

Input files that are required to run this script, including a manifest text file, sample metadata, and the reference sequences and taxonomy from the SILVA 138 small subunit (16S/18S) rRNA database Ref NR 99, are uploaded in the zipped file:

PRJNA860062_InputFiles.zip

FASTQ sequence data for BioSample SAMN29820940, SAMN29820941, SAMN29820942, SAMN29820943, SAMN29820944, and SAMN29820945, can be obtained from the Sequence Read Archive under BioProject PRNJA860062 (https://www.ncbi.nlm.nih.gov/bioproject).

All output files are uploaded in the zipped file:

PRJNA860062_OutputFiles.zip

Data provenance, including the versions of python (3.6.7) and python packages, can be acquired by dragging QIIME2 Visualizations (.qzv output files) into the QIIME2 viewing interface (http://view.qiime2.org).