Bowtie-build @ BioHPC

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).

Bowtie-build builds a Bowtie index from a set of DNA sequences. Bowtie-build outputs a set of 6 files with suffixes .1.ebwt, .2.ebwt, .3.ebwt, .4.ebwt, .rev.1.ebwt, and .rev.2.ebwt. These files together constitute the index: they are all that is needed to align reads to that reference. The original sequence files are no longer used by Bowtie once the index is built.

If you use Bowtie for your published research, please cite the Bowtie paper.

Calculations will be carried out on the BioHPC compute cluster at CBSU. You will receive e-mail notifications when the job is submitted, when it starts, and when it is finished. Output will be available via links embedded in the notification e-mails. For more information about this program and BioHPC interface in general, please visit our Frequently Asked Questions page.

Please acknowledge us in all publications and presentation of work that used our resources using the following text.

You must be a registered user of BioHPC to run Bowtie-build. Please login.

Select input file(s):

Multiple files may be selected by using the left mouse button while holding down the Ctrl key.

Options:

	[ebwt_outfile_base]. Write ebwt data to files with this basename.
	[---nodc]. Disable use of the difference-cover sample. Suffix sorting becomes quadratic-time in the worst case (where the worst case is an extremely repetitive reference). Default: off.
	[-r/--noref]. Do not build the NAME.3.ebwt and NAME.4.ebwt portions of the index, which contain a bitpacked version of the reference sequences and are used for paired-end alignment.
	[-3/--justref]. Build only the NAME.3.ebwt and NAME.4.ebwt portions of the index, which contain a bitpacked version of the reference sequences and are used for paired-end alignment.
	[-o/--offrate <int>]. To map alignments back to positions on the reference sequences, it's necessary to annotate ("mark") some or all of the Burrows-Wheeler rows with their corresponding location on the genome. -o/--offrate governs how many rows get marked: the indexer will mark every 2^ rows. Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime. The default is 5 (every 32nd row is marked; for human genome, annotations occupy about 340 megabytes).
	[-t/--ftabchars <int>]. The ftab is the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first characters of the query. A larger yields a larger lookup table but faster query times. The ftab has size 4^(<int>+1) bytes. The default setting is 10 (ftab is 4MB).
	[--ntoa]. Convert Ns in the reference sequence to As before building the index. By default, Ns are simply excluded from the index and bowtie will not report alignments that overlap them.
	[--seed <int>]. Seed for pseudo-random number generator.

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