Major ITSx update (beta version)

Today, I am very happy to announce that after years in the making and months in testing, the next generation of ITSx, version 1.1, is ready to step into the public light and scrutiny. I have today uploaded a public beta version of the ITSx 1.1 release, which I encourage everyone that have enjoyed using ITSx to try out.

The 1.1 release of ITSx includes a wide range of new feature, including:

• A 2-10x performance increase (depending on the dataset), since ITSx now utilizes hmmsearch instead of hmmscan to detect the ITS regions and distributes the CPU cores better
• Improved ITS detection among fungi and chlorophyta, by addition of new HMM-profiles
• The HMM profile format for ITSx has been updated to HMMER3/f (thus ITSx now requires HMMER version 3.1 or later)
• Better handling of interrupted HMMER searches
• Added the --require_anchor option to only include sequences where the complete anchor is found in the output
• Added the possibility for partial sequence output for the SSU, LSU and 5.8S regions
• Fixed a bug causing problems when reading sequence data from standard input

A lot of the code has changed in this version, which means that there might still be bugs lingering in the program. Since I will be on vacation throughout July, I encourage everyone to submit bug reports and questions, but I will not promise to respond to them until in August.

I hope that you will enjoy this new ITSx release, which you can download here. Happy barcoding!