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. 2011 Aug 1;27(15):2159-60.
doi: 10.1093/bioinformatics/btr325. Epub 2011 Jun 22.

SEAL: a distributed short read mapping and duplicate removal tool

Luca Pireddu  1 , Simone Leo, Gianluigi Zanetti
Affiliations

SEAL: a distributed short read mapping and duplicate removal tool

Luca Pireddu et al. Bioinformatics. .

Abstract

Summary: SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing about 13 GB per hour in map+rmdup mode, while reaching a throughput of 19 GB per hour in mapping-only mode.

Availability: SEAL is available online at http://biodoop-seal.sourceforge.net/.

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Figures

Fig. 1.
Fig. 1.
Throughput per node of the entire SEAL workflow: finding paired reads in different files; computing the alignment; and removing duplicate reads. An ideal system would produce a flat line, scaling perfectly as the cluster size grows. The three datasets used are described in Table 1. By comparison, a single-node workflow we wrote for testing—performing the same work as SEAL but using the standard multithreaded BWA and Picard—reaches a throughput of ~1100 pairs/s on the 5M dataset.
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