2.3.7

• Release version 2.3.7

  General:

  • Fix build on macOS-12 and macOS-13 (Thanks @parham-k!)

2.3.6

• Release version 2.3.6

  General:

  • btllib is now a dependency
  • Documentation updates

  abyss-rresolver-short:

  • btllib source code removed due to btllib now being a dependency

2.3.5

• Release version 2.3.5

  General:

  • Fixed compile errors when using the -DNDEBUG flag.
  • Removed deprecated C++ features.

2.3.4

• Release version 2.3.4

  General:

  • Dropped support for gcc5 due to lack of support for more recent C++ features.

  abyss-rresolver-short:

  • Reduced memory consumption.
  • Better calculation of read size proportions in the input dataset.
  • Increased max read read size allowed.

2.3.3

• Release version 2.3.3

General:

• Fixed a contig overlap distance assertion.

abyss-rresolver-short:

• Multiple read sizes are better handled. E.g. 150 and 151 are processed as one read size.
• Updated default parameters.

2.3.2

• Release version 2.3.2

General:

• Updated the m parameter and the S and N scaffolding parameters to better defaults.

abyss-rresolver-short:

• Updated btllib to 1.1.7

2.3.1

abyss-rresolver-short:

• Fixed a bug that crashed ABySS if Bloom filter size is not specified.
• Fixed a compilation error for clang-10.

2.3.0

• The RResolver algorithm is now part of the default pipeline. RResolver resolves repeats using short reads and generates assemblies with better contiguity and often fewer misassemblies.

rresolver-release

• Added the RResolver component to the ABySS pipeline. This release updates the 2.2.4 ABySS version and is used as a reference for the RResolver manuscript.

2.2.5

Release version 2.2.5

General:

• Resolve various compilation errors in newer versions of clang
• Use ntHash's 0th hash as the default hash instead of the 1st hash
• Added optional RResolver module, not currently part of the ABySS assembly pipeline

abyss-rresolver-short:

• Improves genome assemblies at unitig stage by using a sliding window at read size level
  across repeats to determine which paths are correct
• For further information: consult http://www.birollab.ca/assets/posts/195_Nikolic_Vladimir_HiTSeq_ISMB2020.pdf

misc:

• Extract all tags in a SAM file