Taxonomic diversity assessment using Krona plots.

BLASTp was run (i.e. all metagenomic samples combined in a single assembly) with the metagenomic protein assembly (Megahit) and gene prediction (MetaGeneMark) against the NCBI SwissProt V5 pre-formatted database.


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FILES
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- blastp.outfmt6: BLASTp output format: "6 std staxids"

- krona_megahit_MGM_blastp.html: Interactive HTML Krona plot of all taxonomies ID'd via BLASTp.

- krona_megahit_MGM_blastp.html.files: "Supplemental" files generated by Krona. See "stderr.txt" for specific info.

- krona_tax.lst: Tab-delimited file of BLASTp query ID and corresponding NCBI taxonomy ID

- krona_tax_plots_blast.sh: Bash script to generate Krona plots. See script for details.

- stderr.txt: Krona standard error output.

- stdout.txt: Krona standard output.

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Notebook entries for assembly and gene prediction:

https://robertslab.github.io/sams-notebook/2019/01/02/Metagenome-Assembly-P.generosa-Water-Sample-HiSeqX-Data-Using-Megahit.html

https://robertslab.github.io/sams-notebook/2019/01/03/Gene-Prediction-HiSeqX-Metagenomics-from-Geoduck-Water-Using-MetaGeneMark-on-Mox.html

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Jupyter notebook for BLASTp:

https://github.com/RobertsLab/code/blob/master/notebooks/sam/20190321_swoose_metagnomics_pgen_blastp_ncbi-sp-v5-db.ipynb