# BlobTools Documentation

> Documentation for the BlobTools software

## Guides
- [BlobTools](https://blobtools.readme.io/docs/what-is-blobtools.md)
- [Installation](https://blobtools.readme.io/docs/getting-started.md)
- [Citing BlobTools](https://blobtools.readme.io/docs/citing-blobtools.md)
- [Frequently Asked Questions](https://blobtools.readme.io/docs/frequently-asked-questions.md)
- [BlobTools Workflows](https://blobtools.readme.io/docs/the-blobtools-workflows.md)
- [My first blobplot](https://blobtools.readme.io/docs/my-first-blobplot.md): This section describes the how to generate a BlobPlot based on the files provided in the ```example/``` directory.
- [Taxonomic annotation](https://blobtools.readme.io/docs/taxonomic-annotation.md): How does it work?
- [Coverage parsing](https://blobtools.readme.io/docs/coverage-parsing.md)
- [create](https://blobtools.readme.io/docs/create.md)
- [view](https://blobtools.readme.io/docs/view.md)
- [plot](https://blobtools.readme.io/docs/blobplot-1.md)
- [covplot](https://blobtools.readme.io/docs/covplot-1.md)
- [map2cov](https://blobtools.readme.io/docs/map2cov.md)
- [seqfilter](https://blobtools.readme.io/docs/seqfilter.md)
- [taxify](https://blobtools.readme.io/docs/taxify.md)
- [bamfilter](https://blobtools.readme.io/docs/bamfilter.md)
- [Assembly file](https://blobtools.readme.io/docs/assembly-file.md): Description of assembly file format for use as input files for blobtools
- [Coverage file](https://blobtools.readme.io/docs/coverage-file.md)
- [Hits file](https://blobtools.readme.io/docs/taxonomy-file.md)
- [NodesDB file](https://blobtools.readme.io/docs/taxonomy-database.md)
- [TaxID-mapping file](https://blobtools.readme.io/docs/taxid-mapping-file.md)
- [Taxonomy](https://blobtools.readme.io/docs/taxonomy.md)
- [Taxrule](https://blobtools.readme.io/docs/tax-rule.md)
- [TaxID](https://blobtools.readme.io/docs/taxid.md)
- [Taxonomic rank](https://blobtools.readme.io/docs/taxonomic-rank.md)
- [BlobPlot](https://blobtools.readme.io/docs/blobplot.md)
- [CovPlot](https://blobtools.readme.io/docs/covplot.md)
- [ReadCovPlot](https://blobtools.readme.io/docs/readcovplot.md)