The --rereplicate command would be a good starting point as it accepts only a limited number of options. The manpage could be accessed as such:

man vsearch
man vsearch-rereplicate

Alternatively, per-command help messages (-h or --help) could be easier to find for users not familiar with manpages:

vsearch --help
vsearch --rereplicate --help

The Alignment (Graph) tutorial page makes heavy use of a 3-argument form of addVertex() that takes start position and length parameters in addition to the usual graph parameter. I could not find any such function listed on the Graph docs page (th

The current documentation README is starting to become unwieldy, and it would be nice to have an auto-documented API using Sphinx. A few things to do:

• explain variant types and filters for FastaVariant (#129)
  ...

The current implementation of slice md5 validation proceeds in two steps; it first tries to validate the md5 for the entire slice span. If that fails, it falls back to checking the md5 for a smaller span ([terminating one base earlier](https://github.com/

Currently, learning about the features of bioSyntax and what they translate to involves looking through the manual on our site. If we could package this together with the installation, I think users would be a lot more willing to learn it, especially if we could create custom help text within the editor. e.g. with vim we could possibly [incorporate the manual into the

Rename

• back_coordinate -> ???
• front_coordinate -> ???

Documentation issues:

pointed out by @joergi-w in seqan/seqan3#1093 (review)

• https://github.com/seqan/seqan3/blob/21541d64a4259e97976e71008f63903da7145514/include/seqan3/alignment/all.hpp#L110-L114

  The back coordinate stores the end of the alignment within both sequen

CFFI 1.0 introduced a new out-of-line mode to reduce the overhead when running on CPython.

See:

• http://morepypy.blogspot.com/2015/05/cffi-101-released.html
• https://cffi.readthedocs.org/en/latest/overview.html#out-of-line-example-abi-level-out-of-line

(Wishlist item rather than bug.)

Currently, TileLayout has a set of four containers that all need to be synchronized because they contain different pieces of the same puzzle.

Refactor: Put all synchronized pieces into a single DataSource Object so that mouseover, chunks, download links, layout, and contig spacing can all be coordinated.

1001 Genomes: This will allow me to use MSA code in a Pangenome coordinate frame wit