- correct syntax for >v1 of rasusa
- add contig reorientation using dnaapler
- add careful more for Polypolish
- minor changes to CI testing
- fixed medaka model parsing to allow dots in model name
- Improved documentation on
--ram
- Release to separate Dragonflye to
dragonflye
anddragonflye-gpu
on Bioconda
- add
--prefix
to change final output assembly name - Pilon JVM memory options now controlled by
--ram
- add
--medaka_opts
to allow fine tuning Medaka options
- add
--nanohq
to allow Flye to be run with--nano-hq
- add short reading polishing with Polypolish
- use QC'd reads for final average read length check
- add short read polishing via Pilon
- add gpu support for medaka polishing
- add
-trim
via porechop
- Fix
--list_models
for newer version of medaka - Pin medaka to >v1.5.0 to account for usage change
- add test for
--list_models
to CI
- Adapt
nanoq
parameters tonanoq >- v0.8.1
- Add
--minquality
for quality filtering with nanoq
- Minimap2 uses cpus-1 to account for it using an extra thread for I/O
- Run read length filtering before read depth reduction
- Fix infinite loop that occured
--outdir ./ --force
(./
always exists so it keeps trying ot remove it)
- Fixed coverage handling for Flye
- Miniasm and Raven cannot be filtered by coverage due to these assemblers not outputing contig coverage
- First public release of Dragonflye