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0.8.0
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@paoloczi paoloczi released this 07 Oct 20:45
· 600 commits to master since this release
0.8.0
9bab4d8

Additions and improvements since release 0.7.0

  • Phased diploid assembly via --Assembly.mode 2. Two assembly configurations to facilitate phased diploid assembly for current Oxford Nanopore reads generated by the Guppy 5 base caller are also provided, and can be invoked via --config Nanopore-Phased-Aug2021 (standard reads) or --config Nanopore-UL-Phased-Oct20211 (Ultra-Long reads). These configurations are tentative and are subject to improvements. Please file an issue on the Shasta GitHub repository to discuss unsuccessful assemblies. The documentation page on computational methods includes a description of mode 2 assembly.

  • The --config option is now mandatory. It can specify a Shasta configuration file, as in previous releases, or one of several built-in configurations available within the Shasta executable. Shasta command shasta --command listConfigurations writes a list of available built-in configuration names. Use shasta --command listConfiguration --config name to see details of a specific built-in configuration. A new documentation page describing functionality related to built-in configurations was added.

  • Alignment method 4 (experimental). Selectable via --Align.alignMethod 4. It can be useful for assembly of centromeres.

  • More flexibility in reading fastq files: characters following the plus sign on the third line for each read are now accepted.

  • Additional configuration for assembly of plant genomes. Invoke via --config Nanopore-Plants-Apr2021. Use shasta --command listConfiguration --config Nanopore-Plants-Apr2021 for details.

  • Bayesian consensus callers for Bonito 0.3.1 and Guppy 5.0.7 base callers.

  • Several usability improvements and bug fixes.

Platforms

Linux

  • The shasta-Linux-0.8.0 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. It will not run on Linux systems with older kernels, including CentOS 6, which reached end of support on November 30, 2020.

  • The release includes tar file shasta-Ubuntu-20.04-0.8.0.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-11-0.8.0, for macOS 11.0 (Big Sur). This will only work on Apple systems that use Intel x86-64 processors. Systems with ARM processors, including Apple M1 processors, are not supported.

  • shasta-macOS-10.15-0.8.0, for macOS 10.15 (Catalina). It also runs on macOS 10.14 (Mojave).

Windows

As in previous releases, the Linux executable shasta-Linux-0.8.0 can be used on Windows under Windows Subsystem for Linux (WSL).

ARM

The ARM executable, shasta-Linux-ARM-0.8.0, 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 and m6g.
  • Raspberry Pi Model 4 running 64-bit Ubuntu 20.04.

It will not work on macOS systems with ARM processors, including Apple M1 processors.

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 0.8.0 for postprocessing of an assembly done using a previous release.

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