# 0.1.25

## What's New?
* Added `src/verkkofillet/bin/screen-assembly.sh`, a command-line wrapper around Verkko's `screen-assembly.pl` to standardize contaminant screening inputs and execution.
* Added `src/verkkofillet/bin/rDNA_gap_cleaning.sh`, a utility to replace rDNA-bounded gap regions with a defined `N` block and emit a cleaned FASTA.
* Added pre-run tutorial pages under `docs/tutorials/before_start/`:
  * `run_verkko.md`
  * `check_input.md`

## Key Improvements
* `screen-assembly.sh` now supports built-in help output via `helpme`, `-h`, and `--help`, including argument descriptions and defaults.
* `screen-assembly.sh` validates required runtime tools and input files before launching the downstream Perl workflow.
* `rDNA_gap_cleaning.sh` now includes a per-contig progress bar and writes reproducible processing logs.
* `rDNA_gap_cleaning.sh` now guards against malformed/empty gap coordinates and extraction failures, reducing the risk of truncated FASTA outputs.

## Documentation
* Expanded `docs/tutorials/before_start/check_input.md` with a quantitative coverage definition, explicit formula, practical FASTQ-based coverage commands, and interpretation guidance.
* Revised `docs/tutorials/before_start/run_verkko.md` for clearer scientific language and more explicit use-case framing (basic, trio-informed, and Hi-C-informed modes).