REAL: an efficient REad ALigner for next generation sequencing reads
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Approximate all-pairs suffix/prefix overlaps
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Compression, indexing, and retrieval for massive string data
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
A moldable online scheduling algorithm and its application to parallel short sequence mapping
JSSPP'10 Proceedings of the 15th international conference on Job scheduling strategies for parallel processing
Seed-set construction by equi-entropy partitioning for efficient and sensitive short-read mapping
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Indexing finite language representation of population genotypes
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Journal of Parallel and Distributed Computing
An algorithm for mapping short reads to a dynamically changing genomic sequence
Journal of Discrete Algorithms
DynMap: mapping short reads to multiple related genomes
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Mapping short sequencing reads to distant relatives
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Seed design framework for mapping SOLiD reads
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Approximate all-pairs suffix/prefix overlaps
Information and Computation
A randomized numerical aligner (rNA)
LATA'10 Proceedings of the 4th international conference on Language and Automata Theory and Applications
Unified view of backward backtracking in short read mapping
Algorithms and Applications
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Memory-Aware BWT by segmenting sequences to support subsequence search
APWeb'12 Proceedings of the 14th Asia-Pacific international conference on Web Technologies and Applications
POPE: pipeline of parentally-biased expression
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
Integrating GPU-accelerated sequence alignment and SNP detection for genome resequencing analysis
SSDBM'12 Proceedings of the 24th international conference on Scientific and Statistical Database Management
A randomized Numerical Aligner (rNA)
Journal of Computer and System Sciences
Lyndon fountains and the Burrows-Wheeler transform
Proceedings of the CUBE International Information Technology Conference
High-performance short sequence alignment with GPU acceleration
Distributed and Parallel Databases
WHAM: A High-Throughput Sequence Alignment Method
ACM Transactions on Database Systems (TODS)
Comparing DNA sequence collections by direct comparison of compressed text indexes
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Cache-aware parallel approximate matching and join algorithms using BWT
Proceedings of the Joint EDBT/ICDT 2013 Workshops
Hardware acceleration of genetic sequence alignment
ARC'13 Proceedings of the 9th international conference on Reconfigurable Computing: architectures, tools, and applications
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
Parallel efficient aligner of pyrosequencing reads
Proceedings of the 20th European MPI Users' Group Meeting
Parallel architecture for DNA sequence inexact matching with Burrows-Wheeler Transform
Microelectronics Journal
GapsMis: flexible sequence alignment with a bounded number of gaps
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Multi-pattern matching with bidirectional indexes
Journal of Discrete Algorithms
Frequency-based re-sequencing tool for short reads on graphics processing units
International Journal of Computational Science and Engineering
Hi-index | 3.85 |
Summary: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20–30 times. SOAP2 is compatible with both single-and paired-end reads. Additionally, this tool now supports multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. Availability: http://soap.genomics.org.cn Contact: soap@genomics.org.cn