0.13.0

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.

0.12.0

Additions and improvements since release 0.11.1

• Assembly mode 3.

  • Phased assembly using new computational techniques. A detailed description of computational techniques will become available at a later time.

  • This is a preliminary version, released in this form to encourage experimentation. It has known issues that will be addressed in future releases. Please share your experiences by filing issues in the Shasta GitHub repository.

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

  • Initially only supported for the new high accuracy Oxford Nanopore reads from the 2023.12 data release. It is possible that future releases will also support ONT R10 reads.

  • Invoke using --config Nanopore-ncm23-May2024. This assembly configuration was only tested on human genomes at coverage 40x to 60x, but may be functional at higher or lower coverage, within reasonable limits. It includes limited adaptivity to coverage. Only use with reads of accuracy comparable to the ONT 2023.12 data release.

  • Released with minimal usage documentation.

• New alignment method 5 takes into account k-mer uniqueness when computing an alignment between two reads. Invoke with --Align.alignMethod 5.
  Used by assembly configuration Nanopore-ncm23-May2024.

• Automatic settings of min/max bucket size using a simple heuristics. Invoked by setting both --MinHash.minBucketSize and --MinHash.maxBucketSize to 0. Used by assembly configuration Nanopore-ncm23-May2024.

• Longer markers (command line option --Kmers.k). Maximum allowed marker length is now 31 bases for assembly mode 0 and 30 bases for assembly modes 2 and 3.
  Longer markers become useful as read quality improves.

• New option --Reads.handleDuplicates to deal with reads with duplicate names.
  The default is to keep only one copy of each duplicate read, but other choices are also available.

Platforms

Linux

• The shasta-Linux-0.12.0 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-22.04-0.12.0.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-0.12.0 can be used on Windows under Windows Subsystem for Linux (WSL).

Linux ARM

The ARM executable, shasta-Linux-ARM-0.12.0, 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.

0.11.1

Additions and improvements since release 0.11.0

This is a bug fix release. It contains no new functionality. It includes fixes for the following bugs:

• Issue #4: Using the --Reads.desiredCoverage command line option with an assembly configuration that does not use Run-Length Encoding (RLE) was causing Shasta to terminate with an assertion. This affected all of the 4 recently added assembly configurations for ONT R10 reads.
• Issue #5: Running on some old processors caused Shasta to terminate with an Illegal instruction signal.

Platforms

Linux

• The shasta-Linux-0.11.1 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-22.04-0.11.1.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-0.11.1 can be used on Windows under Windows Subsystem for Linux (WSL).

Linux ARM

The ARM executable, shasta-Linux-ARM-0.11.1, 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 running 64-bit 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 compatible with Shasta 0.11.0, but 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 0.11.1 for postprocessing of an assembly done using a release earlier than 0.11.0.

0.11.0

Additions and improvements since release 0.10.0

• Several new built-in assembly configurations.
  • For human assemblies of ONT R10 reads, fast mode, with one flowcell per genome (low coverage, about 30x):
    • Haploid assembly: Nanopore-R10-Fast-Nov2022.
    • Phased diploid assembly: Nanopore-Phased-R10-Fast-Nov2022.
  • For human assemblies of ONT R10 reads, slow mode, with two flowcell per genome (coverage about 45x):
    • Haploid assembly: Nanopore-R10-Slow-Nov2022.
    • Phased diploid assembly: Nanopore-Phased-R10-Slow-Nov2022.
  • For Ultra-Long (UL) ONT R9 reads at standard coverage (40x to 80x):
    • Phased diploid assembly: Nanopore-UL-Phased-Nov2022.

You can use shasta --command listConfigurations to get a list of all available built-in configurations, and shasta --command listConfiguration --config configurationName to get details of a specific configuration (including comments on applicability).

Platforms

Linux

• The shasta-Linux-0.11.0 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-22.04-0.11.0.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-0.11.0 can be used on Windows under Windows Subsystem for Linux (WSL).

Linux ARM

The ARM executable, shasta-Linux-ARM-0.11.0, 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 running 64-bit 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 0.11.0 for postprocessing of an assembly done using a previous release.