SSPACE – Can’t locate getopts.pl

Today I tried to run the SSPACE Standard perl script for doing scaffolding of pre-assembled contigs, but I got this error message: Can’t locate getopts.pl in @INC (@INC contains: /Tools/SSPACE-STANDARD-3.0_linux-x86_64/dotlib/ /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at SSPACE_Standard_v3.0.pl line 124. getopts.pl is a Perl 4 core library but no longer included in…

How to run velvet with OPENMP

Just few steps to make velvet working for de novo genome assembly using multiple CPU cores: 1) Download the latest version of velvet from http://www.ebi.ac.uk/~zerbino/velvet/ 2) $ tar -xzvf velvet_1.2.10.tgz 3) $ cd velvet_1.2.10 4) Edit the Makefile to compile with a higher Kmer length and enable longsequences for contigs longer than 32kb: $ vim…

ISMB / ECCB 2015

Two poster abstracts of the Bioinformatics group have been accepted at the ISMB/ECCB 2015: Riemenschneider et al.: Multi-label classification for HIV-1 drug resistance prediction Neumann et al.: Non-invasive multivariate prediction model for myocardial infarction Looking forward to Dublin!

Erdös number

I recently checked my Erdös number and it seems that it is 4. But what does that mean? First, Paul Erdös was a mathematician and he published really a lot of scientific papers (>1500) together with a large and broad number of peers. If you want to study connectivity among researchers, you could plot each…

In light of recent events – The flu

The flu (also known as influenza) is an infectious disease caused by a virus – the influenza virus. While most people confuse the flu with the common cold (also an infectious disease, but caused mainly by rhinovirues), the symptoms can be more severe. In fact, the flu can be deadly, especially mutated versions, such as…