Autocycler v0.2.1

This release adds:

• The ability to duplicate sequences with the Autocycler clean command. Particularly useful for linear sequences with terminal inverted repeats.
• The --max_contigs option to Autocycler compress. Helps to catch bad cases early, so as to not waste time.

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.2.1.tar.gz: Linux systems with x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.2.1.tar.gz: Linux systems with x86-64 processors, glibc C standard library
  • I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version.
• Macs:
  • autocycler-macos-x86_64-v0.2.1.tar.gz: Macs with x86-64 Intel processors
  • autocycler-macos-aarch64-v0.2.1.tar.gz: Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files:

• autocycler-documentation-v0.2.1.tar.gz: an HTML copy of the Autocycler docs at the time of release
• autocycler-helper-scripts-v0.2.1.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

Autocycler v0.2.0

This release adds new functionality to facilitate manual completion of assemblies:

• New subcommand: autocycler clean which allows for manual removal of sequences when the consensus assembly is not fully resolved.
• Add depth values to consensus_assembly.gfa file (useful for manual cleaning).

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.2.0.tar.gz: Linux systems with x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.2.0.tar.gz: Linux systems with x86-64 processors, glibc C standard library
  • I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version.
• Macs:
  • autocycler-macos-x86_64-v0.2.0.tar.gz: Macs with x86-64 Intel processors
  • autocycler-macos-aarch64-v0.2.0.tar.gz: Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files:

• autocycler-documentation-v0.2.0.tar.gz: an HTML copy of the Autocycler docs at the time of release
• autocycler-helper-scripts-v0.2.0.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

Autocycler v0.1.2

This release includes some fixes/enhancements in response to feedback from the Autocycler alpha testers:

• Added a check to the assembly helper scripts to ensure that the output prefix is writable.
• Added a genome-size helper script.
• Error messages in helper scripts now print to stderr (not stdout).
• Changed the default value of --count for autocycler subsample to match new instructions.
• Add a message to the end of the autocycler combine stderr to indicate whether or not the assembly appears to be fully resolved.
• Lots of improvements/additions to the documentation.

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.1.2.tar.gz: Linux systems with x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.1.2.tar.gz: Linux systems with x86-64 processors, glibc C standard library
  • I recommend trying the musl version first, as it's more portable. However, if you encounter a memory allocation crash, then try the gnu version.
• Macs:
  • autocycler-macos-x86_64-v0.1.2.tar.gz: Macs with x86-64 Intel processors
  • autocycler-macos-aarch64-v0.1.2.tar.gz: Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files:

• autocycler-documentation-v0.1.2.tar.gz: an HTML copy of the Autocycler docs at the time of release
• autocycler-helper-scripts-v0.1.2.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the v0.1.0 release.

Autocycler v0.1.1

This release includes some fixes/enhancements in response to feedback from the Autocycler alpha testers:

• Fixed a bad version number in the environment.yml file for installing long-read assemblers.
• Added --max_contigs to Autocycler cluster to catch obviously bad input data that could cause the clustering algorithm to hang.
• Improved error messages with empty files.
• Created a helper script for the metaMDBG assembler.
• Allow suppression of terminal colours with an environment variable.
• Additions/refinements to the documentation.

Tarballs of pre-built executable binaries are attached:

• autocycler-linux-x86_64-musl-v0.1.1.tar.gz: for Linux systems with x86-64 processors
• autocycler-macos-x86_64-v0.1.1.tar.gz: for Macs with x86-64 Intel processors
• autocycler-macos-aarch64-v0.1.1.tar.gz: for Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files:

• autocycler-documentation-v0.1.1.tar.gz: an HTML copy of the Autocycler docs at the time of release
• autocycler-helper-scripts-v0.1.1.tar.gz: Autocycler's assembly helper scripts

The Autocycler demo data has not changed, so it can be downloaded from the previous release.

Autocycler v0.1.0

The very first release of Autocycler!

Tarballs of pre-built executable binaries are attached:

• autocycler-linux-x86_64-musl-v0.1.0.tar.gz: for Linux systems with x86-64 processors
• autocycler-macos-x86_64-v0.1.0.tar.gz: for Macs with x86-64 Intel processors
• autocycler-macos-aarch64-v0.1.0.tar.gz: for Macs with Apple silicon processors

There are also some tarballs with cross-platform supporting files:

• autocycler-demo-dataset.tar: Autocycler's demo dataset
• autocycler-documentation-v0.1.0.tar.gz: an HTML copy of the Autocycler docs at the time of release
• autocycler-helper-scripts-v0.1.0.tar.gz: Autocycler's assembly helper scripts