Polypolish v0.6.0

This release of Polypolish includes a few big changes:

• The insert-size filtering step used to be implemented in a separate Python script named polypolish_insert_filter.py. I have now implemented it in Rust with the rest of Polypolish. This is faster and Polypolish now exists as a single executable file with two subcommands:
  • Previously: polypolish_insert_filter.py ..., currently: polypolish filter ...
  • Previously: polypolish ..., currently: polypolish polish ...
• There is a new --careful option which makes Polypolish ignore any read with multiple alignments. This is extra-conservative and recommended for very-low-depth polishing.
• Polypolish used to discard sequence descriptions in its output and it appended _polypolish to the sequence names. Now it retains sequence descriptions and adds polypolish to the end of the description (addresses #7).
  • Previously: >name info → >name_polypolish
  • Currently: >name info → >name info polypolish

There are also a few smaller changes:

• Fixed a bug with determining read orientation, which could result in too many reads being filtered out.
• Removed the polypolish_human_readable.py script, because this now lives here: https://github.com/rrwick/Perfect-bacterial-genome-tutorial/blob/main/scripts/compare_assemblies.py
• Added qscore to estimated accuracy in stderr output.

Tarballs of pre-built executable binaries are attached:

• polypolish-linux-x86_64-musl-v0.6.0.tar.gz: for Linux systems with x86-64 processors
• polypolish-macos-x86_64-v0.6.0.tar.gz: for Macs with x86-64 Intel processors
• polypolish-macos-aarch64-v0.6.0.tar.gz: for Macs with Apple silicon processors

If none of the above work for you, you'll need to build Polypolish from source (see the Installation page on the wiki).