Releases: gbouras13/plassembler
Releases · gbouras13/plassembler
v1.6.2
v1.6.1
v1.6.0
v1.5.1
v1.5.0
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 toplassembler long
andplassembler 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
withplassembler 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 forplassembler 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 tellplassembler
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
withclick
- 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
- Adds option to skip chopper and fastq to
plassembler run
using--skip_qc
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
from v1.1.0. If users want faster runtimes, we recommend--use_raven
or conduct subsampling prior.