Although BWA is a very popular and well tested aligner, it’s hardly the only aligner around. There is an extensive list of open source and commercial short read aligners available on Wikipedia. Another collection can be found on the EBI webpage (there’s also information about the number of citations for each aligner on this page). SeqAnswers has a software collection page as well.
This week I will try two of the most cited (and also oldest) aligners: Bowtie and MAQ.
We have been publishing news, analyses and commentaries about next generation sequencing and HLA typing every single day on Facebook, LinkedIn and Twitter as we see amazing potential in using social media channels for spreading the word about these topics and bioinformatics in general.
We hope to get feedback from you on any of these channels about what topics you would like to hear more about.
No, today is not Talk Like A Pirate Day. “R” is a statistical software (more like an environment) which was inspired by “S” and was originally developed by Robert Gentleman and Ross Ihaka. Nowadays, more than a dozen contributors are working on development and bug fixes. There are also more than 4700 extensions (called “packages” in R-lingo) written and shared by R users.
Although, nothing can replace hands on experience in an actual laboratory, if you don’t have a “wet lab” background and you don’t have a chance to at least visit an actual lab in real life, you can still get a feeling for how things work by taking a look at a virtual laboratory. Of course, in real life everything is much messier, more boring , more tiresome and takes much-much more time. In my experience, Murphy’s law “frequents” labs more than any other place in the whole universe, so everything that can possibly go wrong will actually go wrong at some point. Still, if you want to completely understand a technique or protocol, it helps a lot to go through it step-by-step, even if you just do it virtually. Continue reading
Drumroll! Hurrah! We are finally going to do some alignments today!
BWA is probably the most widely used short read aligner ever. By now, it’s even part of the official Illumina analysis pipeline. BWA actually contains three different aligner algorithms. We’ll try all of these today.
