Cbcb:Pop-Lab:TODO

AMOS

• Create "group" object to sub-cluster sequences/contigs/scaffolds/etc
• Remove iid concept - keep bid and let message files use eids for cross-referencing. this will allow the merging of files
• Remove the layout objects - equivalent with contig without a sequence
• New way to store sequence data targeted at short sequences for which it's too verbose to store names and such
• figure out a way to handle 454 mate-pairs, esp. in hawkeye
• build a better 'toAmos'

Note: some progress in these directions has been made but the changes need to be cleaned up.

AMOScmp

• integrate other aligners - Daniela has a preliminary pipeline that works with SOAP but why not Bowtie? A solution would be to allow inputs in BAM format.

Bambus 2

• Handle scaffolds better than currently done (now the code uses "contigs" instead of scaffolds)
• Write good documentation and put together pipelines for various types of data and underlying assemblers