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.

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

See which versions of smartdenovo are available:

$ module avail smartdenovo

Load one version into your environment and run it:

$ module load smartdenovo/git-5cc1356b
$ smartdenovo.pl -p prefix -c 1 -t 4 reads.fa > prefix.mak
$ make -f prefix.mak

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 SLURM batch job parameters. See the README for more information about the other command line options.

Notes from the sysadmin during installation:

$ 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/*

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