Trycycler v0.5.6

Enhancements/fixes in this release:

• The canu_trim.py script now excludes 'repeat' and 'bubble' contigs.
• Adds --score-N 0 to minimap2 calls to fix compatibility with minimap2 v2.29 and later.
• Fixes a pkg_resources deprecation warning. This has increased Trycycler's minimum required version of Python from 3.6 to 3.9.

Note: Trycycler continues to be maintained for those who prefer or depend on it. However, for most use cases the newer Autocycler is recommended, as it provides the same consensus-assembly approach with better automation and performance.

Trycycler v0.5.5

Just some small fixes and enhancements in this release, including:

• Fix a Pillow deprecation which broke trycycler dotplot (issues #68 and #72).
• Parallelise pairwise alignments for better performance (PR #64, thanks @danpal96).
• All circularisations are now attempted before trycycler reconcile quits with an error. Should help reduce the number of times this command needs to be rerun.

Trycycler v0.5.4

The most significant change in this release affects the final pairwise sequence comparison in Trycycler reconcile. Previously, the maximum pairwise indel size was reported for each sequence pair, but since edlib doesn't do affine-gap alignment, this value wasn't very useful. So I've replaced it with worst-1kbp identity, i.e. the lowest identity across a 1-kbp sliding window. This does a better job of showing how divergent two sequences are at their worst point.

A few other small fixes are also included:

• Better error messages when MUSCLE fails to complete.
• Threading fixes for MUSCLE v5 (though MUSCLE v3 is recommended) - thanks @marade
• Better default thread count when using a scheduler - thanks @EricDeveaud
• Fix bug with finding starting sequences - thanks @menickname

Trycycler v0.5.3

Just one tiny fix in this release: the version number in the tool now correctly matches the version number in GitHub. Thanks to @pvstodghill for catching this one!

Trycycler v0.5.2

Changes since the last version:

• Trycycler now supports the recently released MUSCLE v5.
• Fixed a crash in Trycycler dotplot when no expected fonts were found on the system.

Trycycler v0.5.1

Just a couple little changes in this release:

• Increased the default value of --max_indel_size from 250 to 1000 for trycycler reconcile (#16).
• Fixed a bug where trycycler cluster could crash when trying to save the newick file (#21).

Trycycler v0.5.0

This version adds a new command: trycycler dotplot. This is an optional step which gives a visual representation of the contigs in a cluster. It can help users to make decisions when making decisions during cluster reconciliation.

Trycycler v0.4.3

Just one small fix in this version: previously, Trycycler would crash if any of the input contigs contained a slash character (/) in their name. Now Trycycler checks for this and quits with an error message if it finds a slash. Thanks to @aruginkgo for pointing this out in issue #11.

Trycycler v0.4.2

This release fixes a bug where Trycycler would crash (probably at the MSA step) if any of the input FASTA files had lowercase bases. Thanks to @jdakota1305 for spotting this one: #10.

Trycycler now explicitly uses uppercase bases for all its steps. You can still give it lowercase FASTAs as input, but it will convert them to uppercase.

Trycycler v0.4.1

Just a small change from the previous release: I decided to remove read subset interleaving (for simplicity) and instead interleave the assembler order in the documentation.