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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.

1.0.0 (2023-05-10)

  • 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.

0.1.5 (2023-01-16)

  • 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.

0.1.4 (2023-01-03)

  • 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.

0.1.3 (2022-12-27)

  • Fix bugs in bioconda release - unicycler.py and flye.py conflicts

0.1.2 (2022-12-22)

  • Code refactored.
  • Tests added.
  • Bioconda release.

0.1.1 (2022-08-09)

  • Adds module find plasmids where Flye assembles only 1 complete chromosome.

0.1.0 (2022-08-08)

  • First release