├── .gitattributes ├── .gitignore ├── 16S ├── 16S.pdf ├── README.md └── images │ ├── 16Sgraph.png │ ├── banner.png │ ├── calypso_data_summary.png │ ├── calypso_start.png │ ├── copyrighter.png │ ├── dada_provenance.png │ ├── data_filtering.png │ ├── filter_normalize.png │ ├── next.png │ ├── normalization_tfm.png │ ├── rep_seqs.png │ ├── seq_tree.png │ ├── successful_normalize.png │ ├── successful_parse.png │ ├── successful_parsed_counts.png │ ├── successful_qiime.png │ ├── table_summary.png │ ├── upload_optional_files.png │ └── upload_own_data.png ├── ANVIO ├── ANVIO.pdf ├── README.md ├── images │ ├── aws_rules.png │ ├── inbound.png │ └── outbound.png ├── security.md └── security.pdf ├── AnnotationPipelines ├── AnnotationPipelines.pdf ├── README.md └── images │ ├── new_folder.png │ ├── rast_chooser.png │ ├── rast_job_info.png │ ├── rast_pipeline.png │ └── rast_summ_stats.png ├── AntibioticResistance └── images │ └── resistance.png ├── Assignments ├── Assignments.pdf ├── GenomicsAssignment │ ├── README.md │ └── klebsiella.txt ├── MetagenomicsAssignment │ └── README.md ├── NCBIEDirectAssignment │ ├── README.md │ └── genera.txt └── README.md ├── CITATION.cff ├── CheckM ├── CheckM.pdf ├── README.md └── images │ └── checkm.png ├── Conda └── README.md ├── CrossAssembly ├── CCOM.md ├── CCOM.pdf ├── CrossAssembly.pdf ├── Metabat.md ├── Metabat.pdf ├── README.md └── images │ ├── CCOM.png │ ├── metabat.png │ ├── nineteencontigs.png │ └── spades.png ├── Databases ├── Databases.pdf ├── NCBI_Edirect.md ├── NCBI_Edirect.pdf ├── README.md ├── SRA.md ├── SRA.pdf ├── SRA_WGS_Abstracts.tsv └── images │ ├── 1772048.png │ ├── DDBJ.png │ ├── EMBL.png │ ├── GenBankGrowth.png │ ├── GroundwaterSize.png │ ├── JGI.jpg │ ├── JGI.png │ ├── Mappers.png │ ├── NCBI.png │ ├── NCBIEDirect.png │ ├── TARASize.png │ ├── UniProt.png │ ├── groundwater.png │ ├── kegg.png │ ├── pdb.png │ └── seed.png ├── Datasets ├── .gitattributes ├── CF │ ├── 788707_20171213_S_R1.fastq.gz │ ├── 788707_20171213_S_R2.fastq.gz │ ├── 788707_20180129_S_R1.fastq.gz │ ├── 788707_20180129_S_R2.fastq.gz │ ├── 788707_20180313_S_R1.fastq.gz │ ├── 788707_20180313_S_R2.fastq.gz │ ├── 788707_20181126_S_R1.fastq.gz │ ├── 788707_20181126_S_R2.fastq.gz │ └── README.md ├── Datasets.pdf ├── README.md ├── coral_algae │ ├── Algae.tgz │ ├── CCA.tgz │ ├── Control.tgz │ ├── Coral.tgz │ ├── README.md │ └── fastq │ │ ├── Algae_11.fastq.gz │ │ ├── Algae_12.fastq.gz │ │ ├── Algae_13.fastq.gz │ │ ├── Algae_14.fastq.gz │ │ ├── CCA_11.fastq.gz │ │ ├── CCA_12.fastq.gz │ │ ├── CCA_13.fastq.gz │ │ ├── Control_11.fastq.gz │ │ ├── Control_12.fastq.gz │ │ ├── Control_13.fastq.gz │ │ ├── Control_14.fastq.gz │ │ ├── Coral_11.fastq.gz │ │ ├── Coral_12.fastq.gz │ │ ├── Coral_13.fastq.gz │ │ └── Coral_14.fastq.gz ├── drinking_water │ ├── Calypso │ │ ├── README.md │ │ ├── feature-table.biom │ │ ├── metadata_calypso.tsv │ │ └── taxonomy.tsv │ ├── README.md │ ├── fastq │ │ ├── barcodes.fastq.gz │ │ └── sequences.fastq.gz │ └── metadata.tsv ├── ground_water │ ├── README.md │ └── fastq │ │ ├── SRR3546449_pass_1.fastq.gz │ │ ├── SRR3546449_pass_2.fastq.gz │ │ ├── SRR3546450_pass_1.fastq.gz │ │ ├── SRR3546450_pass_2.fastq.gz │ │ ├── SRR3546451_pass_1.fastq.gz │ │ ├── SRR3546451_pass_2.fastq.gz │ │ ├── SRR3546452_pass_1.fastq.gz │ │ ├── SRR3546452_pass_2.fastq.gz │ │ ├── SRR3546453_pass_1.fastq.gz │ │ ├── SRR3546453_pass_2.fastq.gz │ │ ├── SRR3546454_pass_1.fastq.gz │ │ ├── SRR3546454_pass_2.fastq.gz │ │ ├── SRR3546455_pass_1.fastq.gz │ │ ├── SRR3546455_pass_2.fastq.gz │ │ ├── SRR3546457_pass_1.fastq.gz │ │ └── SRR3546457_pass_2.fastq.gz └── gut │ ├── README.md │ └── fastq │ ├── SRR3466404_pass_1.fastq.gz │ ├── SRR3466404_pass_2.fastq.gz │ ├── SRR3506419_pass_1.fastq.gz │ ├── SRR3506419_pass_2.fastq.gz │ ├── SRR3506420_pass_1.fastq.gz │ ├── SRR3506420_pass_2.fastq.gz │ ├── SRR3546776_pass_1.fastq.gz │ ├── SRR3546776_pass_2.fastq.gz │ ├── SRR3546778_pass_1.fastq.gz │ ├── SRR3546778_pass_2.fastq.gz │ ├── SRR3546779_pass_1.fastq.gz │ ├── SRR3546779_pass_2.fastq.gz │ ├── SRR3546780_pass_1.fastq.gz │ ├── SRR3546780_pass_2.fastq.gz │ ├── SRR3546781_pass_1.fastq.gz │ ├── SRR3546781_pass_2.fastq.gz │ ├── SRR3546782_pass_1.fastq.gz │ └── SRR3546782_pass_2.fastq.gz ├── Deconseq └── README.md ├── Definitions.md ├── FOCUS ├── FOCUS.pdf ├── README.md └── images │ └── focus.jpg ├── GenomePeek ├── GenomePeek.pdf ├── README.md └── images │ ├── metagenome.png │ ├── mixed.png │ └── single.png ├── GenomeSequencingOverview ├── GenomeSequencingOverview.pdf ├── README.md ├── Whole_Genome_Sequencing.pdf └── images │ ├── GenBankGrowth.png │ ├── GenomesOnlineGrowth.png │ └── GenomicsAndModeling.png ├── Hecatomb └── README.md ├── Kraken2 └── README.md ├── LICENSE ├── Linux ├── AWS_SAGC2021_Setup.sh ├── AWS_Setup.txt ├── Linux.pdf ├── MachineSetUp.md ├── MachineSetUp.pdf ├── README.md └── images │ ├── image1.png │ ├── image10.png │ ├── image11.png │ ├── image12.png │ ├── image13.png │ ├── image14.png │ ├── image15.png │ ├── image16.png │ ├── image17.png │ ├── image18.png │ ├── image19.jpg │ ├── image2.png │ ├── image20.png │ ├── image21.png │ ├── image3.png │ ├── image4.png │ ├── image5.png │ ├── image6.png │ ├── image7.png │ ├── image8.png │ ├── image9.png │ ├── mobaxterm_key.png │ └── mobaxterm_ssh.png ├── MMSeqs2 └── README.md ├── Metagenomics ├── AnnotatingOrfMSeed.md ├── AnnotatingOrfMSeed.pdf ├── ExampleDataSets.md ├── ExampleDataSets.pdf ├── Metagenomics.pdf ├── README.md └── images │ ├── 1ng vs 100ng.png │ ├── BAC Cloning.png │ ├── CDA.png │ ├── CDA_Small.png │ ├── Earth Microbiome Project.png │ ├── Filters.png │ ├── Findley_PCA.png │ ├── Handelsman1.png │ ├── Handelsman2.png │ ├── RDP.png │ ├── SSU_RNApol.png │ ├── Silva.png │ ├── Staley_Konopka.png │ ├── Subsystems.png │ ├── VAMPS.png │ ├── Woese_Tree.png │ ├── abrolhos.png │ ├── acridine orange.png │ ├── plate counts.png │ ├── plate_count_anomaly.gif │ ├── qiita.png │ └── who_what_where.png ├── ORFCalling ├── ORFCalling.pdf ├── README.md └── images │ ├── blastx.png │ └── transcription_translation.png ├── PATRIC ├── GenomeSets.md ├── GenomeSets.pdf ├── PATRIC.pdf └── README.md ├── Python ├── .gitattributes ├── Bc01.fasta ├── Bc01.fasta.gz ├── BcSamples.tsv.gz ├── Python_Lesson_00.ipynb ├── Python_Lesson_01.ipynb ├── Python_Lesson_02.ipynb ├── Python_Lesson_03.ipynb ├── Python_Lesson_04.ipynb ├── Python_Lesson_05.ipynb ├── Python_Lesson_06.ipynb ├── Python_Lesson_07.ipynb ├── Python_Lesson_08.ipynb ├── Python_Lesson_09.ipynb ├── Python_Lesson_10.ipynb ├── Python_Lesson_11.ipynb ├── Python_Lesson_12.ipynb ├── README.md ├── Zen_of_python.md ├── countfasta.py ├── countfastq.py ├── metadata.tsv.gz ├── phylum.tsv.gz ├── requirements.txt └── tikkala.gbk.gz ├── README.md ├── RTMg ├── README.md ├── RTMg.pdf └── images │ └── sens.png ├── References ├── README.md └── References.pdf ├── RemovingContamination └── README.md ├── SUPER-FOCUS ├── README.md ├── SUPER-FOCUS.pdf └── images │ └── sf-logo.png ├── SequenceAssembly ├── N50.md ├── N50.pdf ├── README.md ├── SequenceAssembly.pdf └── images │ └── reads_contigs_scaffolds.png ├── SequenceFileFormats ├── INSDC_Features.md ├── INSDC_Features.pdf ├── README.md ├── SequenceFileFormats.pdf └── images │ ├── ascii.png │ ├── crAssphageDNA.png │ ├── crAssphageQuality.png │ ├── fastq.png │ └── prinseq.png ├── SequenceQC ├── IlluminaAdapters.fa ├── README.md ├── SequenceQC.pdf └── images │ ├── BadLength.png │ ├── GoodLength.png │ └── IonTorrentQual.gif ├── Sequencing ├── README.md ├── Sequencing.pdf └── images │ ├── GrowthSRA_SeqCost.png │ ├── SangerCrassphage.png │ ├── SangerCrassphageError.png │ ├── image1.png │ ├── image2.png │ ├── image3.png │ ├── image4.png │ ├── image5.png │ ├── image6.png │ ├── sanger_seq.png │ └── tagmentation.png ├── Snakemake ├── README.md ├── fastp.snakefile ├── filter_assemble.snakefile └── prinseq.snakefile ├── UPDATING.md ├── UPDATING.sh ├── UPGRADE.md ├── Workshops ├── COMBINE_QLD_2024.md ├── 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