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0.10.0

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@paoloczi paoloczi released this 09 May 20:46
· 236 commits to master since this release
0.10.0
e9c39ee

Additions and improvements since release 0.9.0

  • Phased diploid assembly improvements result in more sequence assembled diploid, with larger diploid N50:

    • Algorithmic improvements.
    • Bug fixes.
    • New assembly configurations, listed below.

  • New Bayesian model guppy-5.0.7-b improves repeat count calls on homopolymer repeats for reads generated by the Guppy 5 base caller with "super" accuracy. Used in all new assembly configurations listed below.

  • New assembly configurations:

    • For standard nanopore reads at standard coverage (40x to 80x):
      • Haploid assembly: Nanopore-May2022
      • Phased diploid assembly: Nanopore-Phased-May2022
    • For Ultra-Long (UL) nanopore reads at standard coverage (40x to 80x):
      • Haploid assembly: Nanopore-UL-May2022
      • Phased diploid assembly: Nanopore-UL-Phased-May2022
    • Specialized for human assemblies with one flowcell per genome (low coverage, around 30x):
      • Haploid assembly: Nanopore-Human-SingleFlowcell-May2022
      • Phased diploid assembly: Nanopore-Human-SingleFlowcell-Phased-May2022

  • As announced with release 0.9.0, several items of obsolete functionality were removed.

Deprecated platform (macOS) that will be removed

MacOS support (all versions) is deprecated and will be removed soon. It is likely that this is the last Shasta release that includes macOS support. If you would like this platform to continue to be supported, please file an issue on this repository, with motivation.

Platforms

Linux

  • The shasta-Linux-0.10.0 executable will run on most current 64-bit Linux systems that use kernel version 3.2.0 or later. This includes all Ubuntu versions starting at 12.04 plus CentOS 7 and 8.

  • The release includes tar file shasta-Ubuntu-20.04-0.10.0.tar which is a complete Shasta build on Ubuntu 20.04. It will not be needed by most users.

macOS

Two macOS executables are included in this release:

  • shasta-macOS-11-Intel-0.10.0, for macOS 11.0 (Big Sur) on Apple systems that use Intel x86-64 processors.

  • shasta-macOS-11-ARM-0.10.0, for macOS 11.0 (Big Sur) on Apple systems that use Apple ARM processors, including Apple M1 processors.

Windows

As in previous releases, the Linux executable shasta-Linux-0.10.0 can be used on Windows under Windows Subsystem for Linux (WSL).

Linux ARM

The ARM executable, shasta-Linux-ARM-0.10.0, can be used on 64-bit ARM version 8 platforms. It is known to work at least in the following environments:

  • Graviton2 processors on AWS EC2 instances.
  • 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-0.10.0 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 0.10.0 for postprocessing of an assembly done using a previous release.

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