This release includes a few bug fixes, but most importantly we reworked the mgefinder workflow command.
We broke the command up into three:
mgefinder workflow denovo
mgefinder workflow database
mgefinder workflow custom
The workflow denovo command runs the workflow as it was originally designed and validated in the published study.
The workflow database command runs a workflow that only uses a manually-provided database, and it doesn't use any assemblies. This is useful for when you already know what elements you are looking for.
The workflow custom command allows you to provide a custom snakefile and config files.
We've added an optional --sensitive flag that increases the sensitivity for detecting insertions of elements that create larger direct repeats, up to 50 bp in length. This probably increases the false positive rate, and it may actually slightly reduce sensitivity for to detect elements with smaller direct repeats. It should only be used if you have reads that are larger than much larger than 50 bp in length, 100 bp at a minimum.