  De novo genome assembly is the process of stitching short DNA sequences to
generate longer DNA sequences, without using any reference sequence for
alignment. It enables high-throughput genome sequencing and thus accelerates
the discovery of new genomes. In this paper, we present a toolkit, called
PPA-assembler, for de novo genome assembly in a distributed setting. The
operations in our toolkit provide strong performance guarantees, and can be
assembled to implement various sequencing strategies. PPA-assembler adopts the
popular {\em de Bruijn graph} based approach for sequencing, and each operation
is implemented as a program in Google's Pregel framework for big graph
processing. Experiments on large real and simulated datasets demonstrate that
PPA-assembler is much more efficient than the state-of-the-arts and provides
good sequencing quality.
