We are pleased to announce the release of version 2.2 of the SeqAn library and updated versions of the official SeqAn-based applications. New features include the preliminary addition of a bi-directional FM-Index and a new interface for performing multiple sequence alignments at the same time. The latter uses SIMD features of modern processors to perform up to 16 alignments in parallel per cpu-core (in addition to possible application level multi-threading). Important “under the hood” changes include the replacement of SeqAn’s custom threading framework with C++11’s thread library. This fixes some rare, but long-standing bugs in BAM I/O and improves performance slightly.
There are also major infrastructural changes, including support for the Intel Compiler on all platforms and also experimental support for Clang/C2 on Windows. For the official applications many fixes and improvements to the build system have made all new and optimized binaries possible that work on even more platforms.
All publicly documented interfaces are preserved and no supported platforms where dropped. It is now our policy that this shall not happen in the 2.x cycle anymore at all so you can trust that your applications work with the next releases. Do note, however, that we dropped some interfaces and supported platforms between 2.0 and 2.1.