outcomes.txt

=================
Possible outcomes
=================

Papers/opinion pieces/rundowns
------------------------------

One piece on assembling/improving "large" genomes (euk) -- Lex and Jared.
 - mrc

One piece on metagenome assembly, esp scaling (Nick and Titus)
 * Should I coassemble?
 * completing an assembly reliably
 * getting good strain/variant recovery (sensitivity)
 * getting good/long/accurate contigs (actually ... questionable? in complex environments)
 * 2014 might be the year of pacbio/moleculo long reads for metagenomics ("there is no genome ommmmm")

One piece on what to think about *before* sequencing, and what to expect
(Holly lead?)

One piece on "Truths of assembly"
 - More important to have good data than good assemblers
 - Contamination (either at kit level, or at mixture level) is a fact of life

----

Other potential outputs (blog posts, papers, etc)
-------------------------------------------------

assembly-free evaluation technologies, review/discussion of
 - preqc
 - diginorm stuff

good questions to ask - summary of workshop partitcipant questions (see :doc:`questions`)

an up-to-date paper on assemblies/workflows

pacbio metagenome HMP analysis

benchmarking thoughts

list of data sets!

GENERATION of data sets/Eisen & Bik => standards

web survey of tools ==> Twitter survey

6 months OUTCOMES

table of assemblers <-> citations or opinions on each

one sentence of paragraph and/or "surprise" concepts from each participant

a description of the axes of assembly improvement (genome, diploidy, etc.)
 - scaling
 - contiguity
 - sensitivity/strain variation/diploid assembly

---

Quote:

it would be very useful to have a synthesis of assembly approaches for
metagenomics/non-model organisms and ways in which microbial
ecologists might want to think about their data.  The list of
questions to ask from the first day would be an excellent point of
reference.

Another output could be a 'call-to-arms' describing how the workshop
was organized and the value of hands-on learning from the people who
develop assembly software. Questions I am interested in are: did the
instructors find value in this workshop? Did the 'students'? Are there
plans for follow up with the students? Is the workshop content useful
for those not at the workshop?  --- hard to assess, but the social
media aspect seems to have generated a broader discussion.