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..
introduction
what this is
quick start
one PacBio SMRT cell from ecoli
pipeline (not reference, designed to be read through)
overview
introduce modular pipeline
introduce gkpStore, overlaps, ovlStore, tigStore
read correction
read trimming
unitig construction
local vs grid mode
canu option reference
each option, in detail, grouped by function
canu executable reference
each binary, in detail, alphabetical
option index (alphabetical)
history
Canu
====
.. toctree::
:hidden:
quick-start
faq
tutorial
pipeline
parameter-reference
command-reference
history
`Canu <http://github.com/marbl/canu>`_ is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as
the PacBio RSII or Oxford Nanopore MinION).
Publication
===========
Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM. `Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation <http://doi.org/10.1101/gr.215087.116>`_. Genome Research. (2017).
Install
=========
The easiest way to get started is to download a `release <https://github.com/marbl/canu/releases>`_. If you encounter
any issues, please report them using the `github issues <http://github.com/marbl/canu/issues>`_ page.
Alternatively, you can also build the latest unreleased from github:
::
git clone https://github.com/marbl/canu.git
cd canu/src
make -j <number of threads>
Learn
=========
* :ref:`Quick Start <quickstart>` - no experience or data required, download and assemble *Escherichia coli* today!
* :ref:`FAQ <faq>` - Frequently asked questions
* :ref:`Canu tutorial <tutorial>` - a gentle introduction to the complexities of canu.
* :ref:`Canu pipeline <pipeline>` - what, exactly, is canu doing, anyway?
* :ref:`Canu Parameter Reference <parameter-reference>` - all the parameters, grouped by function.
* :ref:`Canu Command Reference <command-reference>` - all the commands that canu runs for you.
* :ref:`Canu History <history>` - the history of the Canu project.
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