- Refactored codebase and release on pypi
- Adds unit tests and CI
- Replace
argparse
withclick
- Adds option to skip chopper and fastq to
plassembler run
using--skip_qc
- Breaking CLI changes to be compatible with click
plassembler.py
changed toplassembler run
- Adds Raven long read assembly option to
plassembler run
using--use_raven
install_database.py
changed toplassembler 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.
- Fix bugs in bioconda release - unicycler.py and flye.py conflicts
- Code refactored.
- Tests added.
- Bioconda release.
- Adds module find plasmids where Flye assembles only 1 complete chromosome.
- First release