  We propose a new compression scheme for genomic data given as sequence
fragments called reads. The scheme uses a reference genome at the decoder side
only, freeing the encoder from the burdens of storing references and performing
computationally costly alignment operations. The main ingredient of the scheme
is a multi-layer code construction, delivering to the decoder sufficient
information to align the reads, correct their differences from the reference,
validate their reconstruction, and correct reconstruction errors. The core of
the method is the well-known concept of distributed source coding with decoder
side information, fortified by a generalized-concatenation code construction
enabling efficient embedding of all the information needed for reliable
reconstruction. We first present the scheme for the case of substitution errors
only between the reads and the reference, and then extend it to support reads
with a single deletion and multiple substitutions. A central tool in this
extension is a new distance metric that is shown analytically to improve
alignment performance over existing distance metrics.
