BWA @ BioHPC

BWA (Burrows-Wheeler Aligner) is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (target), such as the human reference genome. This web page uses one of the two different algorithms implemented in BWA, designed for short queries up to ~200bp with low error rate (<3%). It does gapped global alignment w.r.t. queries, supports paired-end reads, and is one of the fastest short read alignment algorithms to date while also visiting suboptimal hits. The second algorithm, BWA-SW, designed for long reads with more errors is not yet supported by this submission page.

To use BWA to align your reads to a reference database, the BWA-formatted index of this database must be available. A database is selected using the reference genome index file selector (see below). If the list does not contain the index of the database you need, you will have to first create this index from the FASTA file using the BWA index application (click "Next Gen Tools", on the left, then "BWA index") and then return to this page.

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 BWA. Please login.

Specify reference genome index file:

Don't see the index you need? Use the BWA index application to make one.

Read file(s) type: unpaired reads paired-end reads

Specify read file:
No active registered or pipeline files satisfy the selection criteria

Required program options:

general options
	Name of the output file (extension ".gz" or ".bam" will be appended)
	Create output in BAM format
aln options
	[-n]. Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths.
	[-o]. Maximum number of gap opens
	[-e]. Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps)

samse options
	[-n]. Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written.

sampe options
	[-n]. Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written.
	[-a]. Maximum insert size for a read pair to be considered being mapped properly. Since 0.4.5, this option is only used when there are not enough good alignment to infer the distribution of insert sizes.

Advanced program options (if unsure, leave blank):

aln options:
samse/sampe options:

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