Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L. Salzberg
Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source (http://bowtie.cbcb.umd.edu).
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| Paper | Year | Cited |
|---|---|---|
| Identification of common molecular subsequences | 1981 | 10,144 |
| A Block-sorting Lossless Data Compression Algorithm | 1994 | 2,371 |
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| Algorithms and Data Compression | Computer Science |
| Genomics and Phylogenetic Studies | Biochemistry, Genetics and Molecular Biology |
| RNA and protein synthesis mechanisms | Biochemistry, Genetics and Molecular Biology |
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