History

1.1.0 (2023-06-02)

Refactored codebase and release on pypi
Adds unit tests and CI
Replace argparse with click
Adds option to skip chopper and fastq to plassembler run using --skip_qc
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
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. If users want faster runtimes, we recommend --use_raven or conduct subsampling prior.

Large overhaul.
Adds --pacbio_model for pacbio data
Replaces nanofilt with chopper
Adds -a for assembled mode
Adds subsampling with rasusa, and -s to change subsampling depth, and --no_subsample to turn off subsampling
Adds --keep_fastqs
Adds --keep_chromosome
Refactors mapping code
Adds custom function to identify multimapped reads
Changes output formats - consolidates all output into summary.tsv.

Adds checks for dependencies.
Adds samtools to bioconda recipe (thanks Jan/gaworj).
Adds long-only kmer_mode for very high quality Nanopore reads (R10.4 and above) - experimental until I get more data especially with small plasmids. Does exactly the same (Flye -> Unicycler). Seems to work pretty well.

Adds install_database.py, the Plassembler database and functionality for mapping plasmid contigs to PLDSB.
Update the API to -1 and -2 for short reads, matching Unicycler.
Adds mash as dependency.
Adds plassembler_top_hits_mash_plsdb.tsv output.
Adds plasmid_copy_number_short and plasmid_copy_number_long to fasta header for each plasmid.
Checks dependencies upon initialisation, with message to install Unicycler manually if required.