Data structures: time, I/Os, entropy, joules!
ESA'10 Proceedings of the 18th annual European conference on Algorithms: Part II
Rapid parallel genome indexing with MapReduce
Proceedings of the second international workshop on MapReduce and its applications
Compressed directed acyclic word graph with application in local alignment
COCOON'11 Proceedings of the 17th annual international conference on Computing and combinatorics
Mapping short sequencing reads to distant relatives
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Scalable sequence similarity search and join in main memory on multi-cores
Euro-Par'11 Proceedings of the 2011 international conference on Parallel Processing - Volume 2
Pilot-MapReduce: an extensible and flexible MapReduce implementation for distributed data
Proceedings of third international workshop on MapReduce and its Applications Date
ALAE: accelerating local alignment with affine gap exactly in biosequence databases
Proceedings of the VLDB Endowment
Full-text search on multi-byte encoded documents
Proceedings of the 2012 ACM symposium on Document engineering
Scalable genome scaffolding using integer linear programming
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
Which is faster: bowtie2GP bowtie bowtie2 BWA
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery
Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on GPUs
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Development of a virtualized supercomputing environment for genomic analysis
The Journal of Supercomputing
Privacy-enhanced string matching with wordwise positional sampling
Proceedings of the 8th International Conference on Ubiquitous Information Management and Communication
Hi-index | 3.84 |
Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads 200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk