0.1.25

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).

Contents