Some good and some bad news regarding the PETKit. Good news first; I have written a fourth tool for the PETKit, which is included in the latest release (version 1.0.2b, download here). The new tool is called Pesort, and sorts input read pairs (or single reads) so that the read pairs occur in the same order. It also sorts out which reads that don’t have a pair and outputs them to a separate file. All this is useful if you for some reason have ended up with a scrambled read file (pair). This can e.g. happen if you want to further process the reads after running Khmer or investigate the reads remaining after mapping to a genome.
Then the bad news. There’s a critical bug in PETKit version 1.0.1b. This bug manifest itself when using custom offsets for quality scores (using the –offset option), and makes the Pearf and Pepp tools too strict – leading to that they discard reads that actually are of good quality. This does not affect the Pefcon program. If you use the PETKit for read filtering or ORF prediction, and have used custom offset values, I recommend that you re-run your data with the newly released PETKit version (1.0.2b), in which this bug has been fixed. If you have only used the default offset setting, your safe. I sincerely apologize for any inconveniences that this might have caused.
So Metaxa has gone into the wild, which means that I start to get feedback from users using it in ways I have not foreseen. This is the best and the worst thing about having your software exposed to real-world usage; it makes it possible to improve it in a variety of ways, but it also gives you severe headaches at times. I could luckily fix a smaller bug in the Metaxa code within a matter of hours and issue an update to version 1.0.2. The interesting thing here was that I would never have discovered the bug myself, as I never would have called the Metaxa program in the way required for the bug to happen. But once I saw the command given, and the output, which the user kindly sent me, I pretty quickly realized what was wrong, and how to fix it. Therefore, I would like to ask all out you who use Metaxa to send me your questions, problems and bug reports. The feedback is highly appreciated, and I can (at least currently) promise to issue fixes as fast as possible. We are really committed to make Metaxa work for everyone.
If you have suggestions for improvements, those are welcome as well (though it will take significantly more time to implement new features than to fix bugs). I am currently compiling a FAQ, and all questions are welcome. Finally, I would like to thank everybody who has downloaded and tried the Metaxa package. I can see in the server logs that there are quite many of you, which of course makes us happy.