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 onewarn 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)