Ideas/To Do

This is a rather unsorted list of features that would be nice to have, of things that could be improved in the source code, and of possible algorithmic improvements.

  • show average error rate
  • length histogram
  • --detect prints out best guess which of the given adapters is the correct one
  • warn when given adapter sequence contains non-IUPAC characters

Specifying adapters

Allow something such as -a ADAP$TER or -a ADAPTER$NNN. This would be a way to specify less strict anchoring.

Allow N{3,10} as in regular expressions (for a variable-length sequence).

Use parentheses to specify the part of the sequence that should be kept:

  • -a (...)ADAPTER (default)
  • -a (...ADAPTER) (default)
  • -a ADAPTER(...) (default)
  • -a (ADAPTER...) (??)

Or, specify the part that should be removed:

-a ...(ADAPTER...) -a ...ADAPTER(...) -a (ADAPTER)...

Available letters for command-line options

  • Lowercase letters: i, k, s, w
  • Uppercase letters: C, D, E, F, H, I, J, K, L, P, R, S, T, V, W
  • Deprecated, could be re-used: c, d, t
  • Planned/reserved: Q (paired-end quality trimming), V (alias for –version)