├── .gitignore ├── COPYING ├── MANIFEST.in ├── README.md ├── backyard ├── batch.py ├── report.py └── shrimp_to_sam.py ├── doc ├── Makefile ├── analyse-sample.rst ├── conf.py ├── index.rst ├── polish.rst ├── rnaseq.rst └── variants.rst ├── nesoni ├── CHANGES ├── __init__.py ├── __main__.py ├── annotation.py ├── annotation_tools.py ├── bio.py ├── bowtie.py ├── changes.py ├── clip.py ├── config.py ├── consensus.py ├── consequences.py ├── core.py ├── fill_scaffolds.py ├── fisher_diff.py ├── grace.py ├── graph_layout.py ├── igv.py ├── io.py ├── kmer.py ├── legion.py ├── nesoni-r │ ├── DESCRIPTION │ ├── NAMESPACE │ └── R │ │ ├── basic.R │ │ ├── compare.R │ │ ├── counts.R │ │ ├── fitnoise.R │ │ ├── io.R │ │ ├── nesoni_version.R │ │ ├── nmf.R │ │ └── plotting.R ├── normalize.py ├── nway_diff.py ├── pastiche.py ├── peaks.py ├── recombination.py ├── reference_directory.py ├── reporting.py ├── runr.py ├── sam.py ├── samconsensus.py ├── samcount.py ├── samimport.py ├── samshrimp.py ├── selection.py ├── shred.py ├── shrimp.py ├── span_index.py ├── spanner.py ├── statistics.py ├── storage.py ├── third_party │ ├── __init__.py │ └── vcf │ │ ├── __init__.py │ │ ├── cparse.pyx │ │ ├── filters.py │ │ ├── model.py │ │ ├── parser.py │ │ ├── test │ │ ├── __init__.py │ │ ├── prof.py │ │ └── test_vcf.py │ │ └── utils.py ├── trivia.py ├── variant.py ├── workflows.py ├── working_directory.py └── workspace.py ├── release.py ├── setup.py ├── test ├── data │ ├── NC_001422-malformed.gbk │ ├── NC_001422.fna │ ├── NC_001422.gbk │ ├── NC_001422_modified.fna │ ├── NC_001422_modified.gbk │ ├── counts.txt │ ├── empty.fq │ ├── phi.fa │ ├── phihalf.fa │ ├── phiphi.fa │ ├── reads_1.txt.gz │ ├── reads_2.txt.gz │ ├── test.fa │ ├── test2.fa.bz2 │ ├── test_adaptors.fa │ ├── velvet_test_reads.fa │ ├── velvet_test_reference.fa │ └── velvet_test_reference_modified.fa ├── igv.log ├── modify_sequence.py ├── test_analyse_samples.py ├── test_kmer.py ├── test_legion.py ├── test_nesoni.py ├── 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