├── Figures_scripts ├── Figure_2 │ ├── PUPpy-GUT_community_annotate_Muribaculum_intestinale_wProkka.txt │ ├── PUPpy-GUT_community_primerDesign_script.txt │ ├── PUPpy-GUT_community_pyani.txt │ └── PUPpy-GUT_community_pyani_heatmap_Rscript.Rmd ├── Figure_3 │ ├── PUPpy-MuriPrimers_complex-script │ ├── PUPpy-MuribaculaceaeComplex_16SQIIME2 │ ├── PUPpy-MuribaculaceaeComplex_plot16Sabundance.Rmd │ ├── PUPpy-SSS_community_primerDesign_script │ ├── PUPpy-SSS_community_pyani.txt │ └── PUPpy-SSS_community_pyani_heatmap_Rscript.Rmd ├── Figure_4 │ ├── PUPpy-RelativeAbundanceEstimation_shotgun_16S_data-script.txt │ └── PUPpy_Figure4-quantification_comparisons.Rmd ├── Figure_5 │ ├── PUPpy-insilico_shotgun_sequencing_reads_simulation.txt │ └── PUPpy_Figure5-multiMapping_script.Rmd └── README.md ├── LICENSE ├── README.md ├── conda ├── build.sh ├── meta.yaml └── setup.py ├── images ├── 111223_PUPpy-Figure_1A.png ├── PUPpy-GUI.png ├── PUPpy-PrimerSchematic.png ├── PUPpy_logo_DigitalSchematic.png └── Tropini_Lab_logo.png ├── puppy_env.yml ├── scripts ├── puppy-GUI ├── puppy-align ├── puppy-align_tmp └── puppy-primers └── test ├── INPUT_nonTarget └── Enterocloster_bolteae_ATCC_BAA-613_cds_from_genomic.fna ├── INPUT_primerTarget ├── Bacteroides_ovatus_ATCC_8483_cds_from_genomic.fna └── Bacteroides_thetaiotaomicron_VPI_5482_cds_from_genomic.fna ├── OUTPUT_puppy-align ├── ResultDB.tsv └── align_logfile.txt ├── OUTPUT_puppy-primers_group ├── GroupPrimerTable.tsv ├── IdealGroupGenes.tsv ├── SecondChoiceGroupGenes.tsv ├── UndesiredGroupGenes.tsv └── primer3_files │ ├── Bacteroides_ovatus_ATCC_8483_cds_WP_004291965.1_3356-2-0.tsv │ └── Bacteroides_ovatus_ATCC_8483_cds_WP_004296542.1_2840-2-0.tsv └── OUTPUT_puppy-primers_unique ├── Stats_pipelineOutput.tsv ├── UniqueGenesList.tsv ├── UniqueGenesPlot.pdf ├── UniquePrimerTable.tsv └── primer3_files ├── Bacteroides_ovatus_ATCC_8483_cds_WP_004295683.1_973.tsv ├── Bacteroides_ovatus_ATCC_8483_cds_WP_004297412.1_172.tsv ├── 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