This assembly, version 2.1.4, represents an improvement on the 2.1
chimp assembly by adding in over 300,000 finishing reads,
and merging in 640 finished BACS. There have been
approximately 49,000 additional merges made in this
assembly as compared to the 2.1 assembly.

Sequencing/Assembly: The whole genome shotgun sequence data were
assembled and organized by the Washington University Genome Center.
The underlying whole genome shotgun data were generated at the
Washington University School of Medicine and the Broad Institute.
A 5 megabase region of chromosome 7 was finished at the Washington
University Genome Sequencing Center (chr7:84674857-89461887). The
chromosome Y sequence was finished at the Washington University
Genome Sequencing Center with detailed mapping and extensive
collaboration with David Page's group at the Whitehead Institute
(The DNA Sequence of Chimpanzee Chromosome Y, unpublished; Hughes
et al., Conservation of Y-linked genes during human evolution
revealed by comparative sequencing in chimpanzee. Nature, 2005
437:100-3; PMID:16136134). The chromosome 21 sequence data was
kindly provided by Todd Taylor and the Riken Genome Sciences Center
(Watanabe et al., DNA sequence and comparative analysis of
chimpanzee chromosome 22. Nature. 2004 May27;429(6990):382-8. PMID:
15164055).

This assembly covers about 97 percent of the genome and is based on
6X sequence coverage. It is composed of 192,898 contigs with an N50
length of 44kb, and 33,990 supercontigs with an N50 length of 8.4
Mb.

The whole genome shotgun data from primary donor-derived reads
(Clint, a captive-born male chimpanzee from the Yerkes Primate
Research Center (Atlanta, USA)) were assembled using PCAP (Huang
2006) using stringent parameters derived by eliminating detectable
global mis-assemblies (interchromosomal cross-overs determined by
alignment of the chimpanzee genome against the human genome) larger
than 50kb.

The assembly data were aligned against the human genome at UCSC (B.
Raney) utilizing BLASTZ (Schwartz 2003) to align and score
non-repetitive chimpanzee regions against repeat-masked human
sequence. Alignment chains differentiated between orthologous and
paralogous alignments (Kent 2003) and only 'reciprocal best'
alignments were retained in the alignment set. The chimpanzee AGP
files were generated from these alignments in a manner similar to
that already described (The Chimpanzee Genome Sequencing Consortium
2005). Centromeres were introduced into the chimp sequence at the
positions of the centromeres in the human chromosomes.  Ten
documented/known human inversions (Yunis 1982) supported by the
assembly were introduced into the ordering as was the separation of
alignments to human chromosome 2 into chimpanzee chromosomes 2A and
2B.  We removed the contigs from the WGS project that corresponded
to the finished chromosome 21 and chromosome Y sequences as well as
the contig corresponding to chromosome 7 because they are
represented by the corresponding finished sequences. The chromosome
21 sequence is GenBank Accession Number BA000046 and the chromosome
Y sequence is GenBank Accession Number DP000054.
 
The Nov. 2010 version of chromosome 7, CM000321.3, is assembled
from BACs plus contigs of the previous version of the WGS project,
AACZ02000000.   With the release of  CM000321.3, nearly 700
unlocalized chromosome 7 scaffolds that were redundant with the new
chr7 were suppressed and some AACZ03000000 contigs are not part of
assembly Pan_troglodytes-2.1.3 or Pan_troglodytes-2.1.4.