Manual
Please read manual with installation guide before using SPAdes
Requirements
SPAdes requires a 64-bit Linux system.
Assembling our test multi-cell E. coli dataset by SPAdes uses about 700 Mb peak memory, and single cell
E. coli dataset uses 6 Gb peak memory. Correcting errors in these datasets requires about 70 Gb of RAM.
These datasets can be found at http://spades.bioinf.spbau.ru/spades_test_datasets
Installing SPAdes
1. Installing Debian package (for Debian, Mint, Ubuntu, etc)
First, add the repository containing SPAdes by inserting the following line to the end of the le /etc/apt/sources.list
Note that the space before the last slash is required. Update the package list by typing
sudo apt-get update
After that, SPAdes can be installed just by typing
sudo apt-get install spades
23.2 Installing RPM package (for CentOS, Fedora, Mandriva, Red Hat, SUSE,
etc)
If your Linux system can install RPM packages you can use spades.rpm at http://spades.bioinf.spbau.
ru/release2.0.0/spades.rpm.
3.3 Running SPAdes without installation (building from source)
If you're unable to install a package (e. g. you don't have root privileges), you can download SPAdes as an
archive (http://spades.bioinf.spbau.ru/release2.0.0/spades_2.0.0.tar.gz) and just extract it. In
this case, you will have to take care of some dependencies beforehand:
g++ (version 4.4 or higher)
python (version 2.4 or higher)
cmake (version 2.6 or higher)
boost (version 1.42 or higher)
zlib
3.4 Running SPAdes without installation (even without building)
If you don't have possibility to install some of the packages described above, we've prepared the SPAdes
binaries for multiple values of k (see section 4.4), in the range from 11 to 149. To use these binaries, you
need to download SPAdes as an archive (http://spades.bioinf.spbau.ru/release2.0.0/spades_2.0.
0.tar.gz), extract it and use the following scripts to download the binaries:
./spades_download_binary.py <space-separated values of k>
./spades_download_bayeshammer.py
3.5 Testing your installation
To check your installation type
spades.py
if you intalled SPAdes from package (see 3.1 and 3.2), or
./spades.py
from folder you extracted the archive (see 3.3 and 3.4). It runs SPAdes on a toy dataset ( rst 1;000 bp of
E. coli) that comes with SPAdes for testing purposes. If the installation is successful you will see lines like
the following lines in the end of the log.
*Corrected reads are in .../spades_output/ECOLI_1K/corrected/
*Assembled contigs are .../spades_output/ECOLI_1K/spades_04.18_17.59.30/ECOLI_1K.fasta
*Assessment of their quality is in
.../spades_output/ECOLI_1K/spades_04.18_17.59.30/quality_results/quality.txt
Thank you for using SPAdes!
======= SPAdes pipeline finished
SPAdes works best with new error-correction tool BayesHammer (paper submitted).
SPAdes (version 1.0.0) was initially released only for our collaborators in February 2012 but BayesHammer has not been released yet. Please wait until we release both SPAdes (version 2.0.0) AND BayesHammer (already integretaed into SPAdes pipeline) in the middle of April 2012. You can leave your contact by sending an e-mail to our support and we will notify you about our new release.