Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg | Wisconsin Institute for Discovery

Browsing Posts tagged Site info

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.

Welcome

Comments off

My name is Johan Bengtsson-Palme. I am currently a postdoctoral associate to Jo Handelsman’s lab at the Wisconsin Institute for Discovery, part of the University of Wisconsin-Madison. While in the US, I am on a temporary leave from my position as assistant professor at the Sahlgrenska Academy at University of Gothenburg, Sweden. My research concerns microbiology and microbial ecology, primarily focusing on investigating antibiotic resistance and interactions in bacterial communities through metagenomics and bioinformatics. I also have an interest in molecular taxonomy and improving the quality of reference databases. I work closely with the groups of Joakim Larsson, Jo Handelsman, Erik Kristiansson and Henrik Nilsson. To contact me, feel free to send an e-mail to my firstname.lastname@microbiology.se