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
  • In colorspace and probably also for Illumina data, gapped alignment is not necessary
  • --progress
  • run pylint, pychecker
  • length histogram
  • check whether input is FASTQ although -f fasta is given
  • search for adapters in the order in which they are given on the command line
  • more tests for the alignment algorithm
  • deprecate --rest-file
  • --detect prints out best guess which of the given adapters is the correct one
  • alignment algorithm: make a ‘banded’ version
  • it seems the str.find optimization isn’t very helpful. In any case, it should be moved into the Aligner class.
  • allow to remove not the adapter itself, but the sequence before or after it
  • instead of trimming, convert adapter to lowercase
  • warn when given adapter sequence contains non-IUPAC characters
  • try multithreading again, this time use os.pipe() or 0mq

Specifying adapters

The idea is to deprecate the -b and -g parameters. Only -a is used with a special syntax for each adapter type. This makes it a bit easier to add new adapter types in the feature.

back -a ADAPTER -a ADAPTER or -a ...ADAPTER
suffix -a ADAPTER$ -a ...ADAPTER$
front -g ADAPTER -a ADAPTER...
prefix -g ^ADAPTER -a ^ADAPTER... (or have anchoring by default?)
anywhere -b ADAPTER -a ...ADAPTER... ???
paired (not implemented) -a ADAPTER...ADAPTER or -a ^ADAPTER...ADAPTER

Or add only -a ADAPTER... as an alias for -g ^ADAPTER and -a ...ADAPTER as an alias for -a ADAPTER.

The ... would be equivalent to N* as in regular expressions.

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

Make it possible to specify that the rightmost or leftmost match should be picked. Default right now: Leftmost, even for -g adapters.

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)...

Model somehow all the flags that exist for semiglobal alignment. For start of the adapter:

  • Start of adapter can be degraded or not
  • Bases are allowed to be before adapter or not

Not degraded and no bases before allowed = anchored. Degraded and bases before allowed = regular 5’

By default, the 5’ end should be anchored, the 3’ end not.

  • -a ADAPTER... → not degraded, no bases before allowed
  • -a N*ADAPTER... → not degraded, bases before allowed
  • -a ADAPTER^... → degraded, no bases before allowed
  • -a N*ADAPTER^... → degraded, bases before allowed
  • -a ...ADAPTER → degraded, bases after allowed
  • -a ...ADAPTER$ → not degraded, no bases after allowed

Paired-end trimming

  • Could also use a paired-end read merger, then remove adapters with -a and -g

Available/used letters for command-line options

  • Remaining characters: All uppercase letters except A, B, G, M, N, O, U
  • Lowercase letters: i, j, k, l, s, w
  • Planned/reserved: Q (paired-end quality trimming), j (multithreading)