This track shows the whole genome shotgun (WGS) contigs of the November 2003 Arachne $organism assembly (NCBI Build 1 Version 1) from the Chimp Genome Sequencing Consortium.
The Arachne assembly of sequence to whole genome shotgun (WGS) contigs and the mapping of the contigs to scaffolds (supercontigs) were performed at the Broad Institute. To build this assembly, a "modified de novo" (MDN) assembly was created first, using the human genome to determine — among other things — that particular inserts were not chimeric. A separate "validated chimp-on-human" (VCH) assembly was created by taking the chimp reads that align uniquely to human, forming them into contigs via this alignment, and then removing those contigs that failed a two-haplotype consistency check. Shared reads were then used to align the two assemblies to one another. In positions where the sequence was consistent, it was transferred from the VCH to the MDN assembly, further enriching the latter. Two global misassemblies were manually removed from the merged assembly. This final assembly comprises the Build 1 Version 1 draft release.
The Arachne assembly is composed of 361,782 contigs with an N50 length of 15.7 kb. The total contig length is 2.73 Gb, spanning 3.02 Gb. The assembly contains 37,849 supercontigs (scaffolds) having an N50 length of 8.6 Mb (not including gaps).
ARACHNE: A Whole-Genome Shotgun Assembler. Serafim Batzoglou, David B. Jaffe, Ken Stanley, Jonathan Butler, Sante Gnerre, Evan Mauceli, Bonnie Berger, Jill P. Mesirov, and Eric S. Lander. Genome Research 2002 Jan;12:177-189.
Whole-Genome Sequence Assembly for Mammalian Genomes: ARACHNE 2. David B. Jaffe, Jonathan Butler, Sante Gnerre, Evan Mauceli, Kerstin Lindblad-Toh, Jill P. Mesirov, Michael C. Zody, and Eric S. Lander. Genome Research 2003 Jan;13(1):91-96.