SAND - Scalable Assembly at Notre Dame

SAND is a set of modules for genome assembly that are built atop the Work Queue platform for large-scale distributed computation on clusters, clouds, or grids. SAND was designed as a modular replacement for the conventional overlapper in the Celera assembler, separated into two distinct steps: candidate filtering and alignment.

To use SAND, you start your assembly process as normal, then run a lightweight worker program on as many other machines as you can access. You can start them manually, run them on the cloud, or submit them to systems like Condor or SGE. SAND will organize the machines into a workforce that, under the right conditions, can speed up assembly tasks by several hundred fold.

The correct output of SAND has been validated on the anopheles gambiae, sorghum bicolor, and homo sapiens datasets listed below.

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Sample Data

Sequence Data	Repeat Data	Num Reads	Compr. Size	Notes
small.cfa	small.repeats	101617	21MB	Small subset of Anopheles gambiae.
medium.cfa	medium.repeats	2586385	642MB	Full set of reads from the Anopheles gambiae Mopti form.
large.cfa	large.repeats	7915277	1.7GB	Simulated reads from the Sorghum bicolor genome.
human.cfa	human.repeats	31257852	7.1GB	Ventner Homo sapiens genome.

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