v1.6.2

Bug fix with --force for plassembler download, which will only remove the output directory if --force is specified #49

v1.6.1

• Bug fixes and added tests for --depth_filter which would crash in some scenarios

v1.6.0

• Adds --depth_filter. This will filter out all contigs that have long- (and short-read for plassembler run) read copy numbers that are less than the specified depth filter. Defaults to 0.25x.
• Adds --unicycler_options and --spades_options which allows passing extra Unicycler options (#46 )

v1.5.1

• Fixes #44, where --use_raven was not working (Flye would be used instead). Thanks @wanyuac

v1.5.0

• If you upgrade to v1.5.0, you will need to update the database using plassembler download
• Plassembler v1.5.0 incorporates a new database thanks to the recent PLSDB release 2023_11_03_v2. Thanks @biobrad for the heads up.

v1.4.1 (30 Oct 2023)

Fixes bug with plassembler run, which would exit ungracefully if the isolate had more than 1 chromosome, but no plasmids were recovered by Unicycler (e.g. this vibrio ATCC 17802).

v1.4.0 (2023-10-27)

• Adds --no_chromosome option to plassembler long and plassembler run after a request to allow for the assembly of read sets that have only plasmids.
• Using this will skip Flye and create a dummy 3MB chromosome full of A's and will allow for the downstream completion of Plassembler to recover only the plasmids in your reads.
• Fixes another bug here #37

v1.3.0 (2023-10-24)

• plassembler long should yield improved results. It achieves this by treating long reads as both short reads (in the sense of creating a de Brujin graph based assembly) and long reads (for scaffolding) in Unicycler.
• While I'd still recommend short reads if you can get them, I am now confident that if your isolate has small plasmids in the long read set, plassembler long should find them.
• For more information, see the documentation.
• The ability to specify a --flye_assembly and --flye_info if you already have a Flye assembly for your long reads instead of --flye_directory has been added. Thanks to @incoherentian 's issue
• The ability to specify a --no_copy_numbers with plassembler assembled if you just want to run some plasmids against the PLSDB has been added. Thanks to @gaworj 's issue.

v1.2.0

1.2.0 (2023-09-12)

plassembler v1.2.0 implements the following features:

• plassembler long officially released and implemented using Canu and dnaapler to reassemble unmapped reads in place of Unicycler for plassembler run. While we'd still recommend getting short reads if you really want to recover plasmids, as long as your long reads are short enough (i.e. not size selected), plassembler long should hopefully recover most small plasmids.
• For more information, see the documentation.
• Faster mapping thanks to @fanvanf's issue and solution. Thanks @fanvanf.
• The ability to specify a --flye directory if you already have a Flye assembly for your long reads, which will tell plassembler to skip the long read assembly step.

Full Changelog: v1.1.0...v1.2.0

v1.1.0

• Refactored codebase and release on pypi
• Adds unit tests and CI
• Replace argparse with click
• Breaking CLI changes to be compatible with click
• plassembler.py changed to plassembler run
• Adds Raven long read assembly option to plassembler run using --use_raven
• Adds option to skip chopper and fastq to plassembler run using --skip_qc
• install_database.py changed to plassembler download
• Assembled mode now plassembler assembled
• Untested/experimental long read only mode using plassembler long
• Removes rasusa, -s and --no_subsample from v1.1.0. If users want faster runtimes, we recommend --use_raven or conduct subsampling prior.