Background:

The marmoset (Callithrix jacchus) genome was sequenced to 6X coverage using a female marmoset
(animal id# 186/17066) DNA source kindly provided by Dr. Suzette Tardif, Southwestern National
Primate Research Center (San Antonio, Texas). The DNA source for the CHORI-259 BAC library was
male and the full brother of the female used for whole genome shotgun sequencing (# 186/17066).
The combined sequence reads were assembled using the PCAP software (Genome Res. 13(9):2164-70
2003) and filtered for all known non-marmoset sequence contaminants and unscaffolded singleton 
contigs of less than 2kb in length. This draft assembly is referred to as Callithrix jacchus-2.0.2 
and differs from the previously released 2.0.1 in that 586 reads containing untrimmed 
vector sequence were removed from contig ends. Removal of these reads resulted in 34 contigs less than 
2kb in length.  Those contigs are included in the files posted here. For questions regarding 
this marmoset assembly please visit our existing marmoset genome web page and contact the 
designated person for marmoset. Downloads of the sequence data are available via our genome 
browser FTP server. Funding for the sequence characterization of the marmoset genome was 
provided by the National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH).

Credits:

DNA source - Dr. Suzette Tardif, Southwestern National Primate Research Center, San Antonio, Texas

Sequence assembly - Washington University School of Medicine, Genome Sequencing Center, St Louis, Missouri

CHORI-259 BAC library: Dr. Pieter DeJong, Children's Hospital Oakland Research Institute, Oakland, California

Citation upon use of this assembly in a manuscript:

It is requested that users of this marmoset sequence assembly acknowledge the Washington University
School of Medicine, Genome Sequencing Center in any publications that result from use of this
sequence assembly.

Release notes:

This preliminary assembly is being made available to the community
while the assembly continues to be refined.  This is a draft assembly
with limited quality assessment and thus the data is provided "as is".
Once the assembly has been quality screened, scaffolded and localized
by chromosome, they will be submitted to GenBank and the various
genome browsers.

Assembly details:
*** Contiguity: Contig ***
Total contig number: 282362
Total contig bases: 2929139385 bp
Average contig length: 10374 bp
Maximum contig length: 306810 bp
N50 contig length: 24421 bp
N50 contig number: 33606

Major contig (> 2000 bp) number: 206058
Major_contig bases: 2826765446 bp

Top tier (up to 2500000000 bp): 
  Contig number: 112373
  Average length: 22247 bp
  Longest length: 306810 bp
  Contig bases in this tier: 2500000333 bp
  Top tier N50 contig length: 29214 bp
  Top tier N50 contig number: 25565

Middle tier (2500000000 bp -- 2900000000 bp): 
  Contig number: 139779
  Average length: 2862 bp
  Longest length: 6458 bp
  Contig bases in this tier: 400000653 bp
  Middle tier N50 contig length: 3243 bp
  Middle tier N50 contig number: 43434

Bottom tier (2900000000 bp -- end): 
  Contig number: 30210
  Average length: 965 bp
  Longest length: 1224 bp
  Contig bases in this tier: 29138399 bp
  Bottom tier N50 contig length: 1039 bp
  Bottom tier N50 contig number: 12850



*** Contiguity: Supercontig ***
Total supercontig number: 49724
Average supercontig length: 58908 bp
Maximum supercontig length: 2467257 bp
N50 supercontig length: 298806 bp
N50 supercontig number: 2769

Major supercontig (> 2000 bp) number: 49077
Major_supercontig bases: 2927935869 bp

Scaffolds > 1M: 144
Scaffold 250K--1M: 3373
Scaffold 100K--250K: 4284
Scaffold 10--100K: 13714
Scaffold 5--10K: 8336
Scaffold 2--5K: 19203
Scaffold 0--2K: 670

Top tier (up to 2500000000 bp): 
  Supercontig number: 9399
  Average length: 265989 bp
  Longest length: 2467257 bp
  Contig bases in this tier: 2500031746 bp
  Top tier N50 supercontig length: 357598 bp
  Top tier N50 supercontig number: 2112

Middle tier (2500000000 bp -- 2900000000 bp): 
  Supercontig number: 27973
  Average length: 14300 bp
  Longest length: 71311 bp
  Contig bases in this tier: 400000151 bp
  Middle tier N50 supercontig length: 23214 bp
  Middle tier N50 supercontig number: 4635

Bottom tier (2900000000 bp -- end): 
  Supercontig number: 12352
  Average length: 2357 bp
  Longest length: 2954 bp
  Contig bases in this tier: 29107488 bp
  Bottom tier N50 supercontig length: 2367 bp
  Bottom tier N50 supercontig number: 5522