├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md └── workflows │ └── test-dadaist.yaml ├── .gitignore ├── CITATION.cff ├── Dockerfile ├── LICENSE ├── README.md ├── bin ├── D2-AbundancesPhyloseq.R ├── D2-AlphaDivPhyloseq.R ├── D2-BetaDivPhyloseq.R ├── D2-FilterPhyloseq.R ├── D2-checkLibrary.R ├── D2-checkPhyloseq.R ├── D2-dada copy.R ├── D2-dada-SE.R ├── D2-dada-taxonomy.R ├── D2-dada.R ├── D2-decipher.R ├── D2-importPhyloseq.R ├── D2-updateMetadataPhyloseq.R ├── README.md ├── dadaist2 ├── dadaist2-addTaxToFasta ├── dadaist2-alpha ├── dadaist2-assigntax ├── dadaist2-checkstats ├── dadaist2-console.py ├── dadaist2-crosstalk ├── dadaist2-dada2fasta ├── dadaist2-exporter ├── dadaist2-getdb ├── dadaist2-getdb-legacy ├── dadaist2-importq2 ├── dadaist2-metadata ├── dadaist2-mqc-report ├── dadaist2-normalize ├── dadaist2-phyloseqCheck ├── dadaist2-phyloseqMake ├── dadaist2-phyloseqMake-legacy ├── dadaist2-rundada ├── dadaist2-taxonomy-binning ├── dadaist2-taxplot ├── dadaist2-transposetaxa.py ├── dadaist2-uc2otutab.py ├── installPackages.R ├── rhea-alpha.R ├── rhea-binning.R └── rhea-normalize.R ├── data ├── 16S │ ├── A01_S0_L001_R1_001.fastq.gz │ ├── A01_S0_L001_R2_001.fastq.gz │ ├── A02_S0_L001_R1_001.fastq.gz │ ├── A02_S0_L001_R2_001.fastq.gz │ ├── F99_S0_L001_R1_001.fastq.gz │ └── F99_S0_L001_R2_001.fastq.gz ├── ITS │ ├── P143V_R1.fq.gz │ ├── P143V_R2.fq.gz │ ├── P143Y_R1.fq.gz │ ├── P143Y_R2.fq.gz │ ├── P209_R1.fq.gz │ ├── P209_R2.fq.gz │ ├── clean │ │ ├── P143V │ │ ├── P143Y │ │ └── P209 │ └── primed │ │ ├── P143V_R1.fq.gz │ │ ├── P143V_R2.fq.gz │ │ ├── P143Y_R1.fq.gz │ │ ├── P143Y_R2.fq.gz │ │ ├── P209_R1.fq.gz │ │ ├── P209_R2.fq.gz │ │ └── filtered │ │ ├── P143V_R1.fq.gz │ │ ├── P143V_R2.fq.gz │ │ ├── P143Y_R1.fq.gz │ │ ├── P143Y_R2.fq.gz │ │ ├── P209_R1.fq.gz │ │ └── P209_R2.fq.gz ├── getits.sh ├── merge.fa ├── misc │ └── test.uc ├── phyloseq │ └── phyloseq.rds ├── protocol-16S.json ├── qiime2 │ ├── rep-seqs.qza │ ├── rooted-tree.qza │ ├── table.qza │ └── taxonomy.qza ├── repseqs │ └── rep-seqs.fasta └── wronglabels │ ├── Sample_1_R1.fastq.gz │ ├── Sample_1_R2.fastq.gz │ ├── Sample_2_R1.fastq.gz │ ├── Sample_2_R2.fastq.gz │ ├── Sample_3_R1.fastq.gz │ ├── Sample_3_R2.fastq.gz │ ├── Sample_4_R1.fastq.gz │ └── Sample_4_R2.fastq.gz ├── docs ├── img │ ├── banner.png │ ├── compare-asvs.png │ ├── dadaist-dev.png │ ├── dadaist-figures.zip │ ├── dadaist.png │ ├── dadaist2.png │ ├── flow.pdf │ ├── flow.png │ ├── ma-form.png │ ├── ma-pca.png │ ├── ma-taxa.png │ ├── ma-tools.png │ ├── multiqc.png │ ├── pairs.pdf │ ├── popup.png │ ├── r-bubble.png │ ├── r-taxa.png │ ├── scheme.pdf │ ├── scheme.png │ ├── scheme_small.png │ ├── seqfu-512.png │ └── seqfu-banner.png ├── index.md ├── installation.md ├── introduction.md └── tool │ ├── dadaist2-assigntax.md │ └── dadaist2-tree.md ├── env ├── dadaist2-1.2.4-Darwin.yaml ├── dadaist2-1.2.4-Linux.yaml ├── dadaist2-1.2.5-Darwin.yaml ├── dadaist2-1.2.5-Linux.yaml ├── dadaist2-1.3.0_Linux.yaml ├── dadaist2_1.1.0_Darwin.yaml ├── dadaist2_1.1.0_Linux.yaml ├── dadaist2_1.2.0_Darwin.yaml ├── dadaist2_1.2.0_Linux.yaml ├── new.sh └── strip-env.py ├── lab ├── class │ ├── __pycache__ │ │ └── explib.cpython-39.pyc │ ├── config.ini │ ├── configurator.py │ ├── environment.yml │ ├── explib.py │ ├── microbiome.py │ └── testconf.py ├── dadabot.py ├── dadaist2-getdb.py ├── dadaister.py └── templateR.py ├── meta.yaml ├── multiqc ├── input_tsv_for_transpose.tsv ├── links_mqc.yaml ├── multiqc_data │ ├── multiqc.log │ ├── multiqc_data.json │ ├── multiqc_download_results.txt │ └── multiqc_sources.txt ├── multiqc_report.html ├── table_mqc.yaml └── test_mqc.tsv ├── nextflow ├── README.md ├── bin │ ├── dadaist2-crosstalk │ ├── hclust.py │ ├── transpose.py │ ├── unite-to-usearch.py │ ├── usearch │ └── utax_to_taxonomymatrix.pl ├── nextflow.config ├── simple.nf └── usearch.nf ├── refs └── rdp_train_set_16.fa.gz ├── setup ├── build-conda.sh └── strip-conda.py ├── test ├── R │ ├── D2-importPhyloseq-1.R │ ├── importPhyloseq.R │ └── its-dev.R ├── all.sh ├── auto │ ├── MicrobiomeAnalyst │ │ ├── metadata.csv │ │ ├── rep-seqs.tree │ │ ├── seqs.fa │ │ ├── table.csv │ │ └── taxonomy.csv │ ├── R │ │ └── phyloseq.rds │ ├── dadaist.log │ ├── dadaist2.html │ ├── feature-table.tsv │ ├── metadata.tsv │ ├── rep-seqs-tax.fasta │ ├── rep-seqs.fasta │ ├── rep-seqs.msa │ ├── rep-seqs.tree │ └── taxonomy.txt ├── checkDependencies.R ├── complete.sh ├── dada-stats.pl ├── dadaist-last.txt ├── demux.pl ├── docs.sh ├── docs │ ├── README.md │ ├── dadaist2-crosstalk.pod │ └── dadaist2-mergeseqs.pod ├── filt.R ├── importPhyloseq.dev ├── its │ ├── .gitignore │ ├── amplicons-its.fa │ ├── compare-tax.pl │ ├── join │ │ ├── taxonomy.decipher │ │ ├── taxonomy.tsv │ │ └── taxonomy_summary.png │ ├── ref │ │ └── taxonomy.tsv │ ├── simulate-joined.pl │ ├── simulate_Nlen.sh │ ├── taxonomy.decipher │ ├── taxonomy.tsv │ ├── taxonomy_summary.png │ ├── unite-amplicons.fa │ ├── unite-long550-unique-join.fa │ └── 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