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0.13.0

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@kokyriakidis kokyriakidis released this 13 Sep 16:53
· 154 commits to main since this release
0.13.0
6a28b7b

Additions and improvements since release 0.12.0

  • Assembly configurations for Oxford Nanopore r10.4.1_e8.2-400bps_sup Ultra-Long (UL) reads as announced by ONT in May 2024.

    • Use --config Nanopore-r10.4.1_e8.2-400bps_sup-Herro-Sep2024 for Ultra-Long (UL) error-corrected reads using HERRO.
    • Use --config Nanopore-r10.4.1_e8.2-400bps_sup-Raw-Sep2024 for Ultra-Long (UL) reads without error correction.

  • Assembly mode 3.

    • Several improvements since release 0.12.0.

    • Still a preliminary version, subject to future improvements.

    • Despite the known issues, it produces useful phased assemblies. See this presentation for an analysis of typical assembly results.

    • Used by the two assembly configurations for Oxford Nanopore r10.4.1_e8.2-400bps_sup Ultra-Long (UL) reads listed above.

    • Elapsed time for assembly remains comparable to assembly times in previous Shasta releases. Typical assembly time for a human genome on a machine of appropriate size is 2 to 5 hours.

  • New alignment method 6 takes into account k-mer local and global frequency when computing an alignment between two reads. Invoke with --Align.alignMethod 6. Used by assembly configuration Nanopore-r10.4.1_e8.2-400bps_sup-Raw-Sep2024.conf.

Platforms

Linux

  • The shasta-Linux-0.13.0 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 is statically linked and has no dependencies, so it can be used directly without installation.

  • The release includes tar file shasta-Ubuntu-22.04-0.13.0.tar which is a complete Shasta build on Ubuntu 22.04. It will not be needed by most users.

macOS

As announced with the release of Shasta 0.10.0, macOS versions of Shasta are no longer provided.

Windows

As in previous releases, the Linux executable shasta-Linux-0.13.0 can be used on Windows under Windows Subsystem for Linux (WSL).

Linux ARM

The ARM executable, shasta-Linux-ARM-0.13.0, can be used on 64-bit ARM version 8 platforms. It is known to work at least in the following environments:

  • Graviton, Graviton2, Graviton3 processors on AWS EC2 instances.
  • Raspberry Pi Model 4 or 5 running 64-bit a Debian-derived Linux distribution. This includes Ubuntu.

It will not work on macOS systems with ARM processors.

It is statically linked and has no dependencies, so it can be used directly without installation.

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

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