The Polynerd

Each good scientific experiment should start with an hypothesis. This is true also for sequencing in the age of NGS. However, often enough the data doesn’t fit the expectations. In this case it is of interest to find and mark the violating evidence.

The Ensembl Bacteria database contains more than 2600 whole genomes sequences of Escherichia coli. It should not be a surprise that some of this data will be flawed. As a simple verification I took my own tool for phylogenetic reconstruction, andi, and applied it

Here is a quirks I stumbled upon in modern C++. As an example we will be printing all odd numbers in a vector and the count of odd number so far. For the sake of demonstration I'll be using the following method. #include <

zsh, an alternative to bash, is known for its superior completion system. This provides the user with a convenient way to input arguments and options to a command. It really is a time saver and more tools should come with a completion script. For

For a course on genetic analysis I was required to learn Perl (5). I now spend a week with two books and must say that not only did all my prejudices against Perl come true, it is even worse than I imagined. Where all

Linux allows users to allocate memory via mmap(2). This can then be shrunk, grown, and moved by mremap(2). The feature of the last syscall is that no data actually gets copied. Instead the physical memory pages are simply mapped to different virtual

Die Tage erreichte mich per Mail die folgende Anfrage (persönliche Daten redigiert). Hallo Fabian Kloetzl, für meine Kunden suche ich hochwertige Artikelplätze mit thematischem Bezug. Ein konkretes Interesse meines Kunden auf Ihrer Seite zu buchen besteht bereits. So bin ich auf Ihre Seite aufmerksam

Today, I was trying to validate some user input with C++11's new regular expressions. In essence, I tried the following. auto r = std::regex("[0\\- ]"); std::cout << std::regex_match(some_string, r) << std::endl; The

So richtig funktioniert das alles nicht. Hat jemand eine Idee, was ichvergessen habe? Mich störte schon länger, dass Mails auf meinem Desktop ankamen, bevor sie auf mein Telefon gepusht wurden. Dies konnte ich nun durch den Einsatz von z-push fixen. Dabei habe ich mich

To save battery life I disconnected my Epson PULSENSE watch from my phone for a few days. When I tried to reconnect, I always got the error 20-0101-0008. But finally I managed to do it, here is the trick; disconnect completely: Tell your watch

Bootstrapping has been the de-facto standard for computing support-values of phylogenies for decades; and it has served us well. However, with the rise of high-throughput sequencing its limits became apparent. Not only is it slow, but also the results become less useful, as the

Bit-twiddling on genomes seems to become a regular pattern in this blog; See calculating the gc-content and hashing nucleotides. Today I will go into details on computing the reverse complement. Complementing Ever since the detection of the DNA double helix structure by Watson and