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SPAdes 4.0.0

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@github-actions github-actions released this 04 Jun 04:16
v4.0.0
38af83d

Dear SPAdes community,

Since its birth in 2012 SPAdes has always been a free and open-source software, mainly supported by various academic and non-profit organization grants. However, since 2022 SPAdes is not developed within a certain academic institution anymore. SPAdes is currently maintained and supported by an international group of volunteering contributors, namely, a SPAdes team.

Our old website is not active anymore. We also do not have a dedicated support email. From now on we are relying only on our GitHub repo. Please, download releases and report issues there. SPAdes has revamped documentation available at ablab.github.io/spades/.

SPAdes 4.0 will most likely be the last major release introducing new features and significant changes. No further development is currently planned. Nonetheless, we strongly intend to continue making bug-fix releases and supporting our users. And as always — patches are welcome!

With love and happy assembling
SPAdes team

Full changelog for SPAdes 4.0.0:

  • SPAdes now supports NCBI SRA files as input;
  • Reworked and improved documentation: ablab.github.io;
  • PathRacer - a tool for mapping HMMs to assembly grpah - is now released as a part of SPAdes package;
  • BinSPreader (metagenomic binning refiner) is also released inside SPAdes package;
  • New gfa-split tool for splitting assembly graph into components;
  • New wasterwaterSPAdes mode for quantitative assessment of
    SARS-CoV-2 strains in waste water samples;
  • Python3.8 is now a minimal required version, python2 is deprecated;
  • Native support for running on Apple Silicon processors;
  • Native support for running on aarch64/linux;
  • Binaries are now built using ManyLinux 2.28.
    SPAdes binaries should be compatible with systems using glibc 2.28 and newer including
    ALT Linux 10+, RHEL 9+, Debian 11+, Fedora 34+, Mageia 8+, Photon OS 3.0 with updates, Ubuntu 21.04+.
    In case of any problems we recommend building from sources.
  • Allow external projects integration with SPAdes.
    Projects could be integrated directly with SPAdes codebase or use SPAdes libraries.
    Contact us for technical details.
  • SPAdes outputs assembly graph in GFA v1.2 format by default, older v1.1 format is also available;
  • SPAdes tags circular paths in assembly graph with TP:Z:circular flag;
  • SPAdes internally supports 0 bp overlap graph and graphs with variable overlaps in vertices
    (e.g. multiplex de Bruijn graphs). Some SPAdes standalone tools allow use of such graphs as input.
  • SPAdes now uses zlib-ng for faster gzip decompression of input files;
  • Fixed compilation with gcc 13;
  • Use SPOA for long reads consensus;
  • Parallel & improved GapCloser algorithm;
  • Faster graph simplification;
  • Removed deprecated truSPAdes functionality;
  • Lots of other fixes and improvements.
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