/gannet/Atumefaciens/20190325_blastn_metagenomics_geoduck_metagenemark:

Exploration of metagenomic taxonomic diversity using BLASTn and KronaTools.

BLASTn was run on Mox.

KronaTools was run locally on Sam's computer (swoose) and then added to this folder.

Input FastA for BLASTn is here: http://gannet.fish.washington.edu/Atumefaciens/20190103_metagenomics_geo_metagenemark/20190103-mgm-nucleotides.fa

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FILES

- 20190325_blastn_metagenomics_geoduck_metagenemark.sh: SBATCH script for running BLASTn on Mox.

- blastn.outfmt6: BLASTn output in "format 6". Includes "staxids".

- krona_megahit_MGM_blastn.html: KronaTools HTML file for interactive exploration of taxonomy, derived from BLASTn results.

- krona_megahit_MGM_blastn.html.files: HTML files used by KronaTools to run interactive plot.

- krona_stderr.txt: Standard error from KronaTools command.

- krona_stdout.txt: Standard out from KronaTools command.

- krona_tax.lst: List of NCBI taxonomic IDs from BLASTn out. Used as input for KronaTools.

- krona_tax_plots_blast.sh: Bash script to generate Krona plot.

- slurm-706842.out: SLURM output (i.e. stderr/stdout).

- system_path.log: Contents of Sam's Mox system $PATH.

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Notebook:

https://robertslab.github.io/sams-notebook/2019/03/25/Metagenomics-Taxonomic-Diversity-from-Geoduck-Water-with-BLASTn-and-Krona-Plots.html