Krotman and Yegraliyev et al. 2019

This repository accompanies the publication
Dissecting the factors shaping fish skin microbiomes in a heterogenous inland water system

by

Yaron Krotman, Timur Yergaliyev, Rivka Shani Alexander, Yosef Avrahami and Amir Szitenberg
Dead Sea and Arava Science Center, Dead Sea Branch.

Raw data: Available in the raw_reads directory and under BioProect PRJNA560003.
Workflow: The analysis, from raw data to figures, is layed out in script.ipynb nbviewer.
Supplementary analyses: Avilable in linear_vs_nonlinear.ipynb nbviewer and in test_alpha_diversity_and_rel_abund_group_significance.ipynb nbviewer

Name		Name	Last commit message	Last commit date
Latest commit History 150 Commits
Figures		Figures
NCBI_objects		NCBI_objects
Tables		Tables
concat		concat
dada_outputs		dada_outputs
denoised_tables		denoised_tables
diversity-North		diversity-North
diversity-South		diversity-South
diversity-skin-North		diversity-skin-North
diversity-skin-South		diversity-skin-South
diversity-skin		diversity-skin
diversity-swab		diversity-swab
diversity		diversity
input_qza		input_qza
linear_vs_nonlinear_R2		linear_vs_nonlinear_R2
picrust		picrust
preprint		preprint
raw_reads		raw_reads
significance		significance
trimmed_reads		trimmed_reads
trimmed_reads_singletons		trimmed_reads_singletons
trimmomatic_stats		trimmomatic_stats
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
conda_env_for_bayesian_models_of_faith_pd.yml		conda_env_for_bayesian_models_of_faith_pd.yml
conda_env_for_kernel_PCA.yml		conda_env_for_kernel_PCA.yml
fish_samples_metadata.tsv		fish_samples_metadata.tsv
fish_samples_metadata_loc_code.tsv		fish_samples_metadata_loc_code.tsv
fish_samples_metadata_loc_code_correct_sp.tsv		fish_samples_metadata_loc_code_correct_sp.tsv
git.ipynb		git.ipynb
jgh		jgh
linear_vs_nonlinear.ipynb		linear_vs_nonlinear.ipynb
ncbi_biosample_metadata.tsv		ncbi_biosample_metadata.tsv
ncbi_sra_metadata.tsv		ncbi_sra_metadata.tsv
script.ipynb		script.ipynb
test_alpha_diversity_and_rel_abund_group_significance.ipynb		test_alpha_diversity_and_rel_abund_group_significance.ipynb

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Krotman and Yegraliyev et al. 2019

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