Name
Abstract | ||
|---|---|---|
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 5.4GB 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. le formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1093/bioinformatics/btp336 | BIOINFORMATICS |
Field | DocType | Volume |
Sequence alignment,File format,Alignment-free sequence analysis,Burrows–Wheeler transform,Computer science,Search engine indexing,Software,Bioinformatics,Computer memory,Reference genome | Journal | 25 |
Issue | ISSN | Citations |
15 | 1367-4803 | 252 |
PageRank | References | Authors |
17.05 | 2 | 7 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Ruiqiang Li | 1 | 765 | 91.23 |
| Chang Yu | 2 | 332 | 20.83 |
| Yingrui Li | 3 | 554 | 72.28 |
| Tak-Wah Lam | 4 | 1860 | 164.96 |
| Siu-ming Yiu | 5 | 1026 | 92.90 |
| Karsten Kristiansen | 6 | 487 | 72.62 |
| Jun Wang | 7 | 9228 | 736.82 |