[Seqan-dev] Release of SeqAn 2.4

[Hannes Hauswedell <hannes.hauswedell@fu-berlin.de>]

We are pleased to announce the release of version 2.4 of the SeqAn
library and updated versions of the official SeqAn-based applications.

The alignment module has received significant updates and a parallised
interface. Beyond simple multi-threading the alignment module can
utilise the vector extensions of modern CPUs (SSE4, AVX2, AVX512)
resulting in very impressive speed-ups, especially on long sequences. In
fact speed-ups of ~2000x over the serial case have been measured (AVX512
and 40 threads VS no vectorisation and one thread). The details are due
to be published soon.

The indexing module now also offers a parallelised interface which
distributes multiple searches over the available CPU cores. Furthermore
“optimal search schemes” can now be used for performing even faster
searches with multiple errors. A preprint documenting these algorithms
is available here:
https://arxiv.org/abs/1711.02035

The ReducedAminoAcid module now offers more reductions based on more
recent research and VCF I/O is now compliant to version 4.2 of the
specification, i.e. rows with only eight fields are accepted.

Major work went into fixing SeqAn platform support on non-canonical and
big endian platforms, we are proud that also binary formats like BAM
pass all tests on platforms like PowerPC64 and ARM64. All main release
architectures of Debian GNU/Linux are now well supported and
automatically tested. Sparc64 is one of the few platforms known not to work.

We have improved compatibility with new compilers and the C++17 standard
so SeqAn should generate no warnings in 2018, even with stricter warning
levels.

Finally we would like to announce that this is going to be the last
feature release of SeqAn2. Most of our effort is going into the
development of SeqAn3, now, another announcement will cover this
shortly. Patch-level releases of SeqAn2 may, however, be released if we
find serious bugs or regressions.

*Further links*
Full Changelog: https://github.com/seqan/seqan/blob/master/CHANGELOG.rst
Downloads (also applications): http://packages.seqan.de
Homepage: http://www.seqan.de

-- 
Hannes Hauswedell

PhD candidate
Max Planck Institute for Molecular Genetics / Freie Universität Berlin

address   Institut für Informatik
          Takustraße 9
          Room 019
          14195 Berlin
telephone +49 (0)30 838-75241
fax       +49 (0)30 838-75218
e-mail    hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]