====== smartdenovo ======

SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.

===== Information =====

  * Version: git-5cc1356b
  * Added: March, 2019
  * Link: https://github.com/ruanjue/smartdenovo

===== Usage =====

See which versions of smartdenovo are available:

<code>$ module avail smartdenovo</code>

Load one version into your environment and run it:
<code>$ module load smartdenovo/git-5cc1356b
$ smartdenovo.pl -p prefix -c 1 -t 4 reads.fa > prefix.mak
$ make -f prefix.mak</code>

Note that smartdenovo uses eight CPU threads by default, so please make sure to change that with the ''-t'' option and request the same number of CPUs in your [[https://hpc.ilri.cgiar.org/using-slurm#batch-jobs|SLURM batch job parameters]]. See the [[https://github.com/ruanjue/smartdenovo/blob/master/README.md|README]] for more information about the other command line options.

===== Installation ======

Notes from the sysadmin during installation:

<code>
$ cd /tmp
$ git clone https://github.com/ruanjue/smartdenovo.git
$ cd smartdenovo
$ sed -i -e 's.INSTALLDIR=/usr/local/bin.INSTALLDIR=/export/apps/smartdenovo/git-5cc1356b.' Makefile
$ sudo mkdir -p /export/apps/smartdenovo/git-5cc1356b
$ sudo chown aorth /export/apps/smartdenovo/git-5cc1356b
$ make
$ make install
$ cp *.pl /export/apps/smartdenovo/git-5cc1356b
$ sudo chown root:root /export/apps/smartdenovo/git-5cc1356b/*
</code>

The smartdenovo project does not currently tag their releases with proper versions so I have just used the short git commit hash.