.. _Usage:

Commandline Usage
================================================================================

.. toctree::
   :maxdepth: 2

   tools/AlignSets
   tools/AssemblePairs
   tools/BuildConsensus
   tools/ClusterSets
   tools/CollapseSeq
   tools/ConvertHeaders
   tools/EstimateError
   tools/FilterSeq
   tools/MaskPrimers
   tools/PairSeq
   tools/ParseHeaders
   tools/ParseLog
   tools/SplitSeq
   tools/UnifyHeaders