Tools
=====

Individual tool guides with installation instructions and runnable examples.

.. toctree::
   :maxdepth: 2

   quality-control/index
   alignment/index
   sam-bam-processing/index
   interval-operations/index
   assembly/index
   assembly-qc/index
   annotation/index
   variant-calling/index
   variant-annotation/index
   variant-processing/index
   quantification/index
   differential-expression/index
   single-cell/index
   metagenomics/index
   epigenomics/index
   basecalling/index
   data-access/index
   visualization/index