Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA
sequence reads to large genomes. Bowtie employs a Burrows-Wheeler index with
a novel quality-aware backtracking algorithm that permits mismatches and it is based on the full-text minute-space (FM)
index, which has a memory footprint of only about 1.3 gigabytes (GB) for the human
genome. The small footprint allows Bowtie to run on a typical desktop computer with
2 GB of RAM. The index is small enough to be distributed over the internet and to
be stored on disk and re-used. Multiple processor cores can be used simultaneously
to achieve even greater alignment speed.
Bowtie aligns 35-base pair (bp) reads at a rate of more than 25 million reads per CPU-hour, which is more than 35 times faster than Maq and 300 times faster than SOAP under the same conditions.
Bowtie makes a number of compromises to achieve this speed, but these trade-offs are reasonable within the context of mammalian re-sequencing projects. If one or more exact matches exist for a read, then Bowtie is guaranteed to report one, but if the best match is an inexact one then Bowtie is not guaranteed in all cases to find the highest quality alignment. With its highest performance settings, Bowtie may fail to align a small number of reads with valid alignments, if those reads have multiple mismatches. If the stronger guarantees are desired, Bowtie supports options that increase accuracy at the cost of some performance.
Bowtie is open source http://bowtie.cbcb.umd.edu
Bowtie aligns 35-base pair (bp) reads at a rate of more than 25 million reads per CPU-hour, which is more than 35 times faster than Maq and 300 times faster than SOAP under the same conditions.
Bowtie makes a number of compromises to achieve this speed, but these trade-offs are reasonable within the context of mammalian re-sequencing projects. If one or more exact matches exist for a read, then Bowtie is guaranteed to report one, but if the best match is an inexact one then Bowtie is not guaranteed in all cases to find the highest quality alignment. With its highest performance settings, Bowtie may fail to align a small number of reads with valid alignments, if those reads have multiple mismatches. If the stronger guarantees are desired, Bowtie supports options that increase accuracy at the cost of some performance.
Bowtie is open source http://bowtie.cbcb.umd.edu
No comments:
Post a Comment