Bowtie
Bowtie is an ultrafast, memory-efficient short read aligner for aligning short DNA sequencing reads to large genomes. It is particularly good for aligning reads from technologies such as Illumina, Ion Torrent, and SOLiD sequencing platforms.
dna
sequencing
alignment
genomics
Bowtie: Ultrafast DNA Sequencing Read Aligner
An ultrafast, memory-efficient short read aligner for aligning short DNA sequencing reads to large genomes, optimized for Illumina, Ion Torrent, and SOLiD sequencing platforms.
What is Bowtie?
Bowtie is an open-source tool for aligning short DNA sequencing reads to large genomes. It was developed at Johns Hopkins University and is optimized for speed, memory efficiency, and sensitivity. Some key features of Bowtie include:
- Extremely fast performance - can align 35-basepair reads to the human genome at a rate of over 25 million reads per CPU hour
- Memory efficient - uses a quality-aware, greedy, randomized algorithm to align reads, minimizing memory footprint
- Supports gapped, local, and paired-end alignment modes
- Outputs alignments in SAM format, allowing interoperation with downstream tools like SAMtools
- Allows mismatches and supports configurable mismatch penalties
- Supports both basespace and colorspace (SOLiD) read alignments
Bowtie is implemented in C++ and is commonly used for a variety of RNAseq, ChIP-seq, and DNA-seq experiments that utilize high-throughput sequencing technologies from Illumina, Ion Torrent, SOLiD, and others. It continues to be maintained and updated to handle newer read lengths and sequencing platforms.
Bowtie Features
Features
- Ultrafast alignment of short DNA sequencing reads
- Memory-efficient - low RAM usage
- Supports aligning reads from Illumina, Ion Torrent, SOLiD platforms
- Supports gapped, local and end-to-end alignments
- Output in SAM/BAM format
Pricing
- Open Source
Pros
Very fast performance
Low memory usage allows analyzing large datasets
Supports major short read sequencing platforms
Open source and free to use
Cons
Only for short read alignment, not suitable for long reads
Fewer features than some other aligners
Limited support options since not commercially developed
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