Anchoring millions of distinct reads on the human genome within seconds
Proceedings of the 13th International Conference on Extending Database Technology
MPSCAN: fast localisation of multiple reads in genomes
WABI'09 Proceedings of the 9th international conference on Algorithms in bioinformatics
REAL: an efficient REad ALigner for next generation sequencing reads
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Design of an efficient out-of-core read alignment algorithm
WABI'10 Proceedings of the 10th international conference on Algorithms in bioinformatics
Journal of Parallel and Distributed Computing
Accelerating short read mapping on an FPGA (abstract only)
Proceedings of the ACM/SIGDA international symposium on Field Programmable Gate Arrays
NcRNA homology search using Hamming distance seeds
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Inference of isoforms from short sequence reads
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Unified view of backward backtracking in short read mapping
Algorithms and Applications
JBI'10 Proceedings of the 10th Spanish conference on Bioinformatics for Personalized Medicine
ERNE-BS5: aligning BS-treated sequences by multiple hits on a 5-letters alphabet
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Acceleration of the long read mapping on a PC-FPGA architecture (abstract only)
Proceedings of the ACM/SIGDA international symposium on Field programmable gate arrays
SEME: a fast mapper of illumina sequencing reads with statistical evaluation
RECOMB'13 Proceedings of the 17th international conference on Research in Computational Molecular Biology
Job scheduling for optimizing data locality in Hadoop clusters
Proceedings of the 20th European MPI Users' Group Meeting
Frequency-based re-sequencing tool for short reads on graphics processing units
International Journal of Computational Science and Engineering
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Summary: We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing technology. SOAP is compatible with numerous applications, including single-read or pair-end resequencing, small RNA discovery and mRNA tag sequence mapping. SOAP is a command-driven program, which supports multi-threaded parallel computing, and has a batch module for multiple query sets. Availability: http://soap.genomics.org.cn Contact: soap@genomics.org.cn