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0.9.0
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@0seastar0 0seastar0 released this 03 Feb 19:41
· 413 commits to master since this release
0.9.0
1be3d4c

Additions and improvements since release 0.8.0

  • New implementation of phased assembly (Mode 2) improves the quality of phased assemblies with fewer artifacts (see the documentation for details).

  • Ability to run assemblies without using Run-Length Encoding (RLE) for the reads, especially useful for phased assemblies. RLE encoding is effective for noisy reads, less so for higher-accuracy reads, especially for phased assemblies.

  • New assembly configurations. Use shasta --command listConfiguration --config ??? to list applicability and details of each.

    • Nanopore-UL-Jan2022 (Ultra-Long nanopore reads, haploid assembly).
    • Nanopore-Phased-Jan2022 (nanopore reads, phased diploid assembly).
    • Nanopore-UL-Phased-Jan2022 (Ultra-Long nanopore reads, phased diploid assembly).

  • Many messages useful for performance evaluation previously written to the assembly log output (stdout) are now written to a new file performance.log in the assembly directory, improving the readability of the assembly log.

  • Assembly log output (stdout) is now duplicated to stdout.log in the assembly directory. Use command line option --suppressStdoutLog to suppress this behavior.

  • Several usability improvements and bug fixes.

Deprecated functionality that will be removed

The following functionality is deprecated and will be removed soon. If you would like one of these items to continue to be supported, please file an issue on this repository with motivation.

  • Alignment method 0 (--Align.method 0).

  • Marker graph refinement (--MarkerGraph.refineThreshold).

  • Reverse transitive reduction of the marker graph (--MarkerGraph.reverseTransitiveReduction).

  • Detangle method 1 (--Assembly.detangleMethod 1).

  • Support for macOS 10 (10.15 Catalina and 10.14 Mojave).

  • Ability to build a Shasta AppImage.

Platforms

Linux

  • The shasta-Linux-0.9.0 executable will run on most current 64-bit Linux systems that use kernel version 3.2.0 or later, including all Ubuntu versions starting at 12.04 plus CentOS 7 and 8. It will not run on Linux systems with older kernels, including CentOS 6, which reached the end of support on November 30, 2020.

The release includes tar file shasta-Ubuntu-20.04-0.9.0.tar, a complete Shasta build on Ubuntu 20.04. Most users will not need it.

macOS

This release includes three macOS executables:

  • shasta-macOS-11-Intel-0.9.0, for macOS 11.0 (Big Sur) on Apple systems that use Intel x86-64 processors.

  • shasta-macOS-11-ARM-0.9.0, for macOS 11.0 (Big Sur) on Apple systems that use Apple ARM processors, including Apple M1 processors.

  • shasta-macOS-10-0.9.0, for macOS 10.15 (Catalina). It also runs on macOS 10.14 (Mojave).

Windows

As in previous releases, the Linux executable shasta-Linux-0.9.0 can be used on Windows under Windows Subsystem for Linux (WSL).

Linux ARM

The ARM executable, shasta-Linux-ARM-0.9.0, can be used on 64-bit ARM version 8 platforms. It is known to work at least in the following environments:

  • Graviton2 processors running 64-bit Ubuntu 20.04 on AWS instance types r6g, m6g, c6g, and x2gd.
  • Raspberry Pi Model 4 running 64-bit Ubuntu 20.04.

It will not work on macOS systems with ARM processors, including Apple M1 processors (use shasta-macOS-11-ARM-0.9.0 instead).

Compatibility

This release is not compatible with previous releases. There were incompatible changes in some command line option names, the binary formats used, and the Python API. You cannot use release 0.9.0 for postprocessing of an assembly done using a previous release.

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