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Bowtie is a fast, memory efficient, and sensitive aligner of short DNA reads to longer reference genomes. Bowtie can align single or paired-end reads of length 35 to 100 and provides high-throughput alignments. Bowtie 2 supports gapped alignments and unpaired reads. Bowtie 2 supports alignments against genomes or paired-end reads that have been indexed with Burrows-Wheeler aligner (BWA) version 0.5.9. This aligner maps short sequence reads and identifies sequencing or alignment errors. This program comes in 3 editions: main program, command line tools and stand alone.
Main features:
• Fast. Bowtie is extremely fast; able to align 35bp reads to reference genome in half the time it takes to align 75bp reads.
Supported formats:
– aligners: Bowtie, Bowtie 2, Burrows-Wheeler aligner (BWA) and FM Indexed SAM
Required dependencies:
– **BWA** >= 0.5.9 – only for Bowtie 1.
– **Bowtie** – only for Bowtie 2
– **FM Indexed SAM** – for Bowtie 1 and Bowtie 2
– **SAMtools** – for Bowtie 1 and Bowtie 2
Frequently asked questions:
1. How do I run Bowtie?
$ bowtie
You will be prompted for the input file in the SAM format.
To run Bowtie on multiple CPUs, specify the number of CPUs using the -t argument. For example:
$ bowtie -t 4
To run Bowtie for a specific genome, specify the path to the genome using the -p argument. For example:
$ bowtie -p /path/to/genome/file
2. How do I use Bowtie?
$ bowtie -a [OPTIONAL] [–] [
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OS: Windows 7, 8, or Windows 10 (64-bit required)
Processor: 2.4 GHz or faster processor with 4 GB RAM
Graphics: Microsoft DirectX 11 graphics card or equivalent
Hard Drive: 17 GB of free disk space
DirectX: Version 9.0c
Network: Broadband Internet connection
Additional Notes: This version of GunnerPro does not support the original Xbox 360 model controllers.
New Features:
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Access the GunnerPro online multiplayer game lobby from within Windows
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