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Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

SimilarTo.png: Bwa

Suggests.pngsuggests : bowtie2

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Please refer to the [bowtie1 manual] for more detailed information.
The code used to be downloaded from sourceforge[1] but recently moved to GitHub [2]

Handicon.png Current version of the Illumina's iGenomes cufflinks annotation files were obtained (here: [3]) and is documented (here: [4]). Importantly, These annotation files are augmented with the tss_id and p_id GTF attributes that Cufflinks needs to perform differential splicing, CDS output, and promoter user analysis.


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