├── .dockerignore ├── .gitattributes ├── .github └── workflows │ ├── dockerhub-deploy.yml │ └── pytest-integration.yml ├── .gitignore ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── data └── .gitignore ├── docker ├── bbtools-license ├── mlr-license ├── spades-license └── starcode-license ├── docs ├── Bench-Protocol-with-RCA.md ├── Bench-Protocol.md ├── Experimental-Validation.md ├── Installation.md ├── Pipeline-Details.md ├── README.md └── Running-the-Analysis-Pipeline.md ├── img ├── coverage-rank.png ├── cumulative-wells-sequenced.png ├── gpcr-frac-coverage.png ├── octopus-logo.png └── overview.jpg ├── pipeline └── .gitignore ├── protocol └── README.md ├── requirements.txt ├── src ├── background.fasta ├── bc-contam.py ├── flatten-fasta.py ├── guided-assembly.sh ├── igenomx-meta.txt ├── jgi-denovo.sh ├── jgi-preproc.sh ├── link-data.py ├── main.py ├── reorient-fasta.py ├── variant-calling.sh └── vcf-parse.py └── test ├── pOK_barcode-aggregated-stats.tsv ├── pOK_barcode_test ├── Data │ └── Intensities │ │ └── BaseCalls │ │ ├── Plate01_S6_L001_R1_001.fastq.gz │ │ ├── Plate01_S6_L001_R2_001.fastq.gz │ │ ├── Plate02_S7_L001_R1_001.fastq.gz │ │ └── Plate02_S7_L001_R2_001.fastq.gz ├── SampleSheet.csv └── input.fasta ├── seq_dirs ├── no_fastqs │ ├── SampleSheet.csv │ └── ref.fa ├── no_ref │ ├── Data │ │ └── Intensities │ │ │ └── BaseCalls │ │ │ └── test.fastq.gz │ └── SampleSheet.csv ├── no_samp │ ├── Data │ │ └── Intensities │ │ │ └── BaseCalls │ │ │ └── test.fastq.gz │ └── input.fa └── not_dir └── test_pipeline.py /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/octantbio/octopus/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/octantbio/octopus/HEAD/.gitattributes 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