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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.



See which versions of smartdenovo are available:

$ module avail smartdenovo

Load one version into your environment and run it:

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

See the README for more information.


Notes from the sysadmin during installation:

$ cd /tmp
$ git clone
$ 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.

smartdenovo-software.1553197138.txt.gz · Last modified: 2019/03/21 19:38 by aorth