Autocycler v0.6.0

This release updates the logic for how Autocycler resolve chooses the best path when creating bridges. Previously, it simply chose the most common path, but this was sometimes suboptimal at loci where the input assemblies are very diverse. Now it chooses the medoid (the path with the minimum distance to all other paths) which should be more robust.

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.6.0.tar.gz: x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.6.0.tar.gz: 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-v0.6.0.tar.gz: x86-64 Intel processors
  • autocycler-macos-aarch64-v0.6.0.tar.gz: Apple silicon processors

An HTML copy of the Autocycler docs at the time of release is also attached: autocycler-documentation-v0.6.0.tar.gz

Autocycler v0.5.2

This release includes:

• Performance improvements for Autocycler cluster – faster execution and less RAM usage.
• New --min_depth option for Autocycler clean
• Bash pipeline now includes a time limit on assembly jobs (thanks, @muntean-alex)

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.5.2.tar.gz: x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.5.2.tar.gz: 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-v0.5.2.tar.gz: x86-64 Intel processors
  • autocycler-macos-aarch64-v0.5.2.tar.gz: Apple silicon processors

An HTML copy of the Autocycler docs at the time of release is also attached: autocycler-documentation-v0.5.2.tar.gz

Autocycler v0.5.1

Just a few additions/fixes in this release:

• Added hifiasm to Autocycler helper.
• Added a new header hint: autocycler_ignore
• Fixed error in Dockerfile (thanks, @ppenev-eligo)

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.5.1.tar.gz: x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.5.1.tar.gz: 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-v0.5.1.tar.gz: x86-64 Intel processors
  • autocycler-macos-aarch64-v0.5.1.tar.gz: Apple silicon processors

An HTML copy of the Autocycler docs at the time of release is also attached: autocycler-documentation-v0.5.1.tar.gz

Autocycler v0.5.0

The main change in v0.5.0 is that the helper scripts have now been integrated into Autocycler as a built-in subcommand:

• Instead of running canu.sh, you now run autocycler helper canu.
• This simplifies installation – no more copying Bash/Python scripts.
• The new autocycler helper command also adds features:
  • Support for Myloasm.
  • Support for different read types (e.g. PacBio HiFi).
  • Better cleanup of empty assemblies that could break pipelines.
  • Per-contig read depths where possible, with filtering options.
  • Output .log files when produced by the assembler

Other updates:

• Fixed bug with passing_clusters column in clustering.tsv file (thanks, @MrTomRod).
• Added new columns to clustering.tsv for contig header hints.

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.5.0.tar.gz: x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.5.0.tar.gz: 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-v0.5.0.tar.gz: x86-64 Intel processors
  • autocycler-macos-aarch64-v0.5.0.tar.gz: Apple silicon processors

an HTML copy of the Autocycler docs at the time of release is also attached: autocycler-documentation-v0.5.0.tar.gz

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

Autocycler v0.4.0

This release contains:

• Added ways to influence Autocycler via input contig headers.
• Autocycler cluster terminal output now shows topology information, to show which contigs are circular vs linear.
• A new Plassembler helper script, which can help to recover small plasmids that other long-read assemblers often miss.
• Updated my full Autocycler pipeline to use Plassember and the new input contig headers. Also limits threads to 128 to prevent Flye from crashing (thanks @samlipworth).

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.4.0.tar.gz: x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.4.0.tar.gz: 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-v0.4.0.tar.gz: x86-64 Intel processors
  • autocycler-macos-aarch64-v0.4.0.tar.gz: Apple silicon processors

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

• autocycler-documentation-v0.4.0.tar.gz: an HTML copy of the Autocycler docs at the time of release
• autocycler-helper-scripts-v0.4.0.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 v0.3.0

This release contains:

• A new gfa2fasta command for converting Autocycler graphs to FASTA format.
• A fix for compatibility with BandageNG (see #17).
• Changed terminology for linear sequences: 'open' instead of 'blunt' for non-hairpin ends. This is because 'blunt' might imply a lack of overhang, which is not necessarily true, so 'open' is a more general term.

Tarballs of pre-built executable binaries are attached:

• Linux:
  • autocycler-linux-x86_64-musl-v0.3.0.tar.gz: x86-64 processors, musl C standard library
  • autocycler-linux-x86_64-gnu-v0.3.0.tar.gz: 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-v0.3.0.tar.gz: x86-64 Intel processors
  • autocycler-macos-aarch64-v0.3.0.tar.gz: Apple silicon processors

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

• autocycler-documentation-v0.3.0.tar.gz: an HTML copy of the Autocycler docs at the time of release
• autocycler-helper-scripts-v0.3.0.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 v0.2.1

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.