SRP008449 chicken W project Identification of avian W-linked contigs by short-read sequencing Avian W chromosomes have proved difficult to assemble with whole genome shotgun methods, creating a demand for novel approaches to identify W-linked sequence contigs. We apply a novel method for identifying sequences that are W-specific. Using the Illumina Genome Analyzer, we generated sequence reads from a male domestic chicken (ZZ) and mapped them to the existing female (ZW) genome sequence. This method allowed us to identify segments of the female genome that are underrepresented in the male genome and are therefore likely to be female specific. We developed a Bayesian classifier to automate the calling of W-linked contigs and successfully identified more than 70 novel W-specific sequences. Our classifier can be applied to improve heterogametic whole-genome shotgun assemblies of the W or Y chromosome of any organism. This study greatly improves our knowledge of the W chromosome and will enhance future studies of avian sex determination and sex chromosome evolution.