Background:  For this genome, originally estimated to be 
480 Mb, fosmid and plasmid libraries were constructed using 
genomic DNA purified from whole animals of the S2F2 line, 
which was clonally derived from a single animal. Recently, 
Spencer Johnston of Texas A&M University estimated the size 
at ~800 Mb. This draft assembly contains read pairs from 
plasmid libraries from both adult and a juvenile genomic 
DNA plus a fosmid library (322,506 reads) equivalent to 
11.60X Q20 sequence coverage of the genome.  The PCAP.rep
whole genome assembler was used (Huang et al, Nucleic Acids 
Res. 2006 Jan 5;34(1):201-5).  Additional filtering following 
assembly removed contigs less than 2000 bases as well as 
potential contaminants.  186381 supercontigs (including 
singletons) were removed by this process, with 43,294 
supercontigs remaining.

This genome has proven to be A/T rich (69%), very repetitious
(46% of total genome), and heterozygous (even though the
animals used for DNA preparation were clonally derived) having 
portions that recombine, making automated assembly of the genome
very difficult. BAC library preparations have been unsuccessful, 
as the DNA degrades during the preparation process.  The genome 
size calculated using this assembly is ~ 865 Mb (compared to the 
newly estimated 800 Mb size).  We are supplying this draft 
assembly to the public, but caveat emptor. 


Production Assembly Stats:

project: planaria_060701
total reads input: 14661609
total reads placed: 11608032
total reads unplaced: 3053577
chaff rate: 0.21

total input phred20 bases: 9278500353
estimated genome size: 800000000
total contig length added sum: 1043913544
phred20 bases sequence redundance: 11.60 X
total input reads bases: 11046874141
average phred20 per read: 632.84
average read length: 753.46

total contig number: 94682
maximum contig length: 289494
major contig (> 2kb) number: 71200

total supercontig number: 43294
maximum supercontig length: 672495
major supercontig (> 2kb) number: 43294

based on the added contigs sum:
contig N50 length: 19025
contig N50 number: 11081

based on the added supercontigs sum:
supercontig N50 length: 40862
supercontig N50 number: 5080

total GC counts in the genome: 258862322 (30%)
total AT counts in the genome: 606718679 (70%)
total NX counts in the genome:      6039 ( 0%)

total mate pairs forward reverse constraints: 6925300
total unsatisfied constraints excluding due to singleton,
short supercontig, and supercontigs end: 196791
total unsatisfied rate: 2.84 %