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. To use BWA, the specially formatted index of the reference database must be available. This web page allows you to build such an index from a set of reference DNA sequences in FASTA format. Once the index is built, it will be available for selection on the BWA submisison 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.

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You must be a registered user of BioHPC to run BWA index. Please login.

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Select input file (reference genome in FASTA format):      


-- select file(s) --Brachypodium_distachyon_Bd21.main_genome.scaffolds.fastamaize_agp_v2.fasta.gz

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Options:     

[-p] Index files produced will have this basename (*required*) is bwtsw [-a] Algorithm for constructing the index Register the calculated index for future use within BioHPC (recommended) Enter short description of the index to be registered: Cluster: This application can't run at this time - no suitable clusters or you are not authorized to use the service. The service is available only to Cornell students, faculty, and staff.   ( Show timeout info )

Messages: Cluster Athena under maintenance: Cluster biosim operating normally Cluster biosim2K8 operating normally Cluster cbsum2k8 operating normally Cluster cbsusrv05 operating normally Cluster cbsulm01 under maintenance: Cluster CAC_v4_lease under maintenance: Cluster biosim_linux operating normally Cluster cbsuss04 operating normally Cluster cbsum1c1b001 operating normally Cluster cbsum2 operating normally Application P-IPRSCAN under maintenance: