Sequence assembly

From TipperWiki

• 23 assemblers
• Automated scoring
  • amosvalidate high level discussion, collection of tools. not comparative across assemblers?
  • A Machine Learning Approach to Genome Assembly Validation - poster that mentions "comparison of two assemblies made by different assemblers"
• Human review
  • Genome Assembly Validation - mentions "most popular assemblers"
    • Hawkeye - AMOS assembly viewer
    • asmQC - Detection of correlated mate-pair violations
    • C-E statistic - Compression/expansion statistics for mate-pair violations
    • findTcovSNPs - Detection of correlated polymorphisms
  • C.A.Ve. - Contig Assembly Verifier
• Misc
  • NCBI Assembly Archive

16:45 <@pyrimidine> deafferret: (checked backlog and saw your comment)
                    Bio::Assembly needs some helping hands, might be worth
                    plumbing that code prior to writing up your own stuff.
16:46 <@deafferret> pyrimidine: roger that. I'll check it out thoroughly before
                    I go too crazy on my own tangents  :)
16:47 <@deafferret> not familiar with what that namespace does already
16:47 <@pyrimidine> basic classes for contigs, scaffolds, etc
16:47 <@pyrimidine> including IO
16:47 <@pyrimidine> though it needs some refactoring
16:47 <@deafferret> ah. that could be very helpful as I harness each
                    assembler...
16:47  * deafferret is full of pipedreams today
16:48 <@pyrimidine> it has a lot of useful stuff, just needs to be reworked to
                    handle a common SeqFeature database (one per assembly
                    instead of one per scaffold)
16:56  * pyrimidine remembering Bio::Assembly is also part of the Align
          overhaul (http://www.bioperl.org/wiki/Align_Refactor)