The following are notes from Pat Minx about the WUGSC Oxytricha Mac genome assemblies.

2.0 PCAP assembly w/ 3730 reads, have not located the parameters or the PCAP version
========================================================================================
2.1 Consed autoedited, manually improved,

Reason for new Assembly: autoedited version of 2.0 Oxytricha_trifallax
-------------------------------------------
Note: assembly 2.1 is autoedited.
Oxytricha_trifallax-2.1_060712.pcap.all.ace.fixed.tag
is the improved version by sorting.

====================================================================
2.1.1 more 3730 reads added

** Assembly Description ***

Organism: Oxytricha_trifallax
Ticket#:  26327
Assemby version: 2.1.1
Round Autofinish: na
Finished date: 8/1/06
Assembled by: K. Kim (kkyung@watson.wustl.edu)
Reason for new Assembly: new reads manually added to 2.1 version. (does not include 454 [mrna] data.
=======================================================================
2.1.2 454 reads added (8 sff files)

*** Assembly Description ***

Organism: Oxytricha_trifallax
Ticket#:
Assemby version: 2.1.2
Round Autofinish: na
Finished date: 2/10/09
Assembled by: K. Kim (kkyung@watson.wustl.edu)
Reason for new Assembly: Ran add454Reads.perl on 2.1.1 ace file.

=======================================================================
2.1.3 added singletons not assembled in 2.0
*** Assembly Description ***

Organism: Oxytricha_trifallax
Ticket#:
Assemby version: 2.1.3
Round Autofinish: na
Finished date: 090323
Assembled by: N. Thane (nthane@watson.wustl.edu)
Reason for new assembly: Added 3730 singletons reads from 2.0 assembly

=======================================================================
2.1.4 Added 52 additional sff files
*** Assembly Description ***

Organism: Oxytricha_trifallax
Ticket#:
Assemby version: 2.1.4
Round Autofinish: na
Finished date:
Assembled by:
Reason for new assembly: Added 454 datasets using
add454Reads.perl:


=======================================================================
2.1.5 manually added reads not assembled by add454Reads.perl script

*** Assembly Description ***

Organism: Oxytricha_trifallax
Ticket#:
Assemby version: 2.1.5
Round Autofinish: na
Finished date:
Assembled by:
Reason for new assembly: Manually adding in reads that did not go in during the 2.1.4 attempt


=======================================================================
2.1.6  This assembly has contaminants removed from 2.1.5 version.


=======================================================================
2.1.7   Manually remove singletons and contigs less than 500 bp from 2.1.6 assembly

=======================================================================
2.1.8
The purpose of this assembly is to merge 2.1.7 and 9.0 assemblies together. The
9.0 is the assembly of all the most recent 454 data, which is the 3-5Kb region
I believe. We could not do addNewReads with the reads (too many), so we
assembled them first.

We made consensus fake reads out of all contigs and scaffolds of 9.0 assembly
that were less than 2KB (4 contigs) and added them in manually (ie, not
assembled them in).

Big contigs and scaffolds of 9.0 were manually merged in

We removed many fake reads from 9.0 major contigs because they did not align
correctly.  They and a group of reads that did not go in during add new reads
were added in as singletons:

I renamed the acefiles below to the name following it for distribution purposes
to the collaborator. So they are equivalent - 2.1.8A is major contigs and
2.1.8B is small contigs.

This assembly was screened and 963 contigs of lamprey (Petromyzon marinus) were
removed.