seqan/seqan — pull request #435 by holtgrewe (2014-07-10 15:46:29+00:00)
Title: Update to consensus module and seqcons.

This pull request contains an updated version of the `consensusAlignment()` function from the `consensus` module an an updated version of the `seqcons` app. The `consensusAlignment()` function contains code from the ANISE insert assembler.

Ultimately, `seqcons2` should replace `seqcons`. A release of `seqcons` exists on http://packages.seqan.de, but we could also add a tag here before the replacement.

The `consensusAlignment()` function should be replaced by the new version.

The only thing missing in `seqcons2` is the undocumented FASTA file format from the `consensus` module which is a deletion candidate IMO and support for the AMOS format. The latter should be fairly easy to support through the store module.

However, when advertising `seqcons2` as a drop-in replacement for the Celeara Assembler, we need to test this and probably need an expert with CA. I do not know whether `seqcons` v1 works correctly with the AMOS format and I propose that we should only consider supporting AMOS when someone requests this.