The Gorilla gorilla gorilla whole genome shotgun (WGS) project has the project accession CABD00000000. This version of the project (02) has the accession number CABD02000000, and consists of sequences CABD02000001-CABD02465847.
- 2.1x WGS capillary sequenced read pairs.
- 35x Solexa sequenced read pairs with insert sizes 150 bp and 450 bp. All sequence was derived from DNA sampled from a single female Western Lowland gorilla (Gorilla gorilla gorilla), Kamilah.
Assembly invvolved several phases, starting with a de novo assembly of the initial data using the ABySS and Phusion assemblers. Contigs from this 'seed' assembly were then grown by assembling and attaching Solexa read pairs from the initial data. To improve long-range structure, supercontig construction was guided by placing (where possible) seed contigs in accordance with their homologous locations on the human genome, breaking supercontigs wherever a potential break between human and gorilla was inferred in an alignment of all the Solexa data to human.
This draft assembly contains all the assembled supercontigs plus a mitochondrial sequence. Of the assembled supercontigs there are three types:
1. Placed supercontigs, assembled from seeds (capilliary read contigs) placed in accordance with human synteny.
These are named e.g. chr1_12345_67890, meaning a supercontig of length 67890 roughly syntenous with a region on human chromosome 1 starting at 12345.
2. Unplaced supercontigs, assembled from seeds which did not place on human. These are named e.g. unplaced1234_1_5678, meaning a supercontig of length 5678. There are about 47000 of these.
3. Cut fragments identified as potential initial misassemblies when stitching together placed contigs. These are named e.g. cut_chr1_12345_678 meaning a fragment of length 678, initially assembled from seeds placed near to 12345 on human chromosome 1. The mitochondrial sequence is derived from a gorilla MT sequence in the trace archive. Polymorphisms specific to Kamillah were incorporated during a final phase of the assembly.
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