V1.2.0

Coverage:

• Changes Filtlong downsampling for faster Rasusa (and now purely random)
• Uses downsampled reads for coverage analysis to speed up alignment phase (default: maximum 30X coverage)
• Option to set fold coverage parameter --coveragemax
• Skip downsampling by setting --coveragemax to 0
• Use Mosdepth for calculating coverage from alignments (and removing need to resort)

Meryl/Merqury:

• Adds user-modifiable parameters for meryl (--merylkmer and --merylmem)
• Adds ability to input local meryl database (--meryldb)

Adds option to input local BUSCO database (--localbuscodb)

CRAQ/Correctness:

• Reduced mapping redundancy by proving CRAQ with pre-aligned reads also used for coverage analysis (and checked for consistency with default CRAQ alignment)
• Post-installation edits of CRAQ scripts (runSR.sh and runLR.sh) to add multithreading during samtools depth

Adds --resume option for runs

Can now use regular expressions as input for --telomererepeat

Add memory per thread option during samtools sort (--sortmem)

Quast is now multithreaded

Added multithreaded pigz compression after downsampling

v1.1.0

Updated conda package to include all R packages including ggradar and removing installation check during script run

Adding --sequences option to disitnguish between assemblies to be kept scaffolded or broken into contigs for all subsequent analyses. Previously it was a mix of both scaffolds and contigs.

Fixed paqplot issues with library installation

Fixed paqplot issues with variables being plotted

Modified paqplot variable for plotting (e.g. remove underscores for the plots, change labelling scheme)

v1.0.0-beta

Version 1 release of PAQman

Contains both functions paqman.sh and paqplot.sh

v0.0.1-beta

Zenodo reference release

Added Apptainer/singularity image

Added coverage_normal(%) stat to paqman output
Updated paqplots to handle coverage_normal(%) stat