Microbiology, Metagenomics and Bioinformatics

I’ve been informed by my web service provider that there will potentially be downtime of this site on the 13th of February (Wednesday this week), due to a server upgrade. I hope this will cause as little trouble as possible (both for you and for me).

You know the feeling when your assembler supports paired-end sequences, but your FASTQ quality filterer doesn’t care about what pairs that belong together? Meaning that you end up with a mess of sequences that you have to script together in some way. Gosh, that feeling is way too common. It is for situations like that I have put together the Paired-End ToolKit (PETKit), a collection of FASTQ/FASTA sequence handling programs written in Perl. Currently the toolkit contains three command-line tools that does sequence conversion, quality filtering, and ORF prediction, all adapted for paired-end sequences specifically. You can read more about the programs, which are released as open source software, on the PETKit page. At the moment they lack proper documentation, but running the software with the “–help” option should bring up a useful set of options for each tool. This is still considered beta-software, so any bug reports, and especially suggestions, are welcome.

Also, if you have an idea of another problem that is unsolved or badly executed for paired-end sequences, let me know, and I will see if I can implement it in PETKit.

I have reorganised my Software page a little bit, putting the smaller scripts on a separate page, to make the main software page tidier. The content of the pages is the same, and you still find bloutminer and metaorf on the main software page.

My name is Johan Bengtsson-Palme. I am doing research in microbiology and microbial ecology, primarily focusing on investigating antibiotic resistance of bacterial communities through the use of metagenomics and bioinformatics. I also have an interest in systems biology, and mathematical modelling of biological systems. I am currently a member of Joakim Larsson’s group at the Sahlgrenska Academy, and reside in Gothenburg on the Swedish west coast. To contact me, feel free to send an e-mail to my firstname.lastname@microbiology.se