Claviceps

This release includes a major update: it's now possible to run all the combinations of reads type (merged or R1R2), k-mer strategies (manual, kmergenie or reads_length) and assemblers (spades, megahit, masurca, minia, abyss, sparseassembler) in a single run. All these combinations can be switched on and off from the config file and there is now one single Snakefile. To run the workflow using merged reads is no longer necessary to use Snakefile_merged.
The output directory structure significantly changed from previous version to reflect the changes that allow to run all the above mentioned configurations in a single run.

Additional minor update: fastk is always run using R1R2 reads to allow merquryFK to spot erroneous k-mers derived from the merging process.

Boletus

The major change in this release is the substitution of Pilon with pypolca for assembly improvement.

Upgraded packages:

Package	v_1.0.0 saccharomyces	v_1.1.0 cordyceps	v_2.0.0 boletus
merquryfk	1.1.2	--	1.1.3
masurca	4.1.3	--	4.1.4

Cordyceps

This release includes the following improvements:

• workflow/rules/seqkit_merged.smk has been added to estimate the k-mer size from the median length of merged reads, rather than using R1, when using workflow/Snakemake_merged.
• the script coverage_viz.py has been updated to improve the visualisation of the distributions. Now it always uses logarithmic scale.
• some post-workflow scripts have been added.
• the handling of resources (memory, cpus) has been updated to improve the workflow efficiency.

Saccharomyces

This is the first release of FSP_assembly_benchmarking! 🍄
The workflow is fully functional and ready to use.