SRA

This is the initial deposit of data from the genome of the Puerto Rican parrot (Amazona vittata) that is being sequenced and assembled in an international collaboration supported by many individual donations from the people of Puerto Rico. A. vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the territory of the United States, and the first parrot belonging to the large Neotropical genus Amazona to be studied on a genomic scale. The sequencing was initiated with the construction of two genome libraries: a short fragment library (~300 bp inserts) for sequencing the majority of the genome, and a long fragment library (~2.5 kb inserts) to generate scaffolds to be used to order and assemble contigs derived from the short fragment library. Raw Illumina HiSeq reads were processed and filtered using the Genome Analyzer Pipeline software provided by the manufacturer set to the default parameters. 86.48% of the 309,060,168 paired-end reads and 85.14% of the 180,079,956 mate-pair reads generated passed Illumina quality control (QC). Based on the total number of base pairs generated, a total coverage depth of 26.89X of the parrot's genome. The assembly was conducted by Ray software and consists of 358,398 contigs (>100 bp) and 245,947 scaffolds (>100 bp).