Sequence Analysis

What is UA HPC/HTC and how do I use it?

For large scale analyses,  use UA High Performance/High Throughput Computing systems. See the UA HTC FAQs

How do I run BLAST on UA HPC/HTC?

See the BLAST FAQ

What tools are available for NGS data analysis?

For mapping, there are modules for bwa, bowtie2, and unsupported modules for smalt  and Stampy (see below for info on unsupported modules.)  There is a version of MosaikAligner in /genome/ICEbin.

For de novo assembly of genomic data, there are modules for velvet, SOAPdenovo, and ABySS.

For transcriptome assembly, there are modules for oases and trinity.

What are unsupported modules and how do I use them?

Unsupported modules may be installed by UA HPC users after requestion permission by emailing HPC-Consult AT list DOT arizona DOT edu.  To see the unsupported modules already installed, run the command:

        ls  /unsupported/*/*

To use an unsupported module, run the commands:

        module  load  unsupported

        module  load  group/program/version

How do I run bowtie/tophat/cufflinks on UA HPC?

See the FAQ HERE

How can I annotate my microbial project?

For annotation of bacterial genomes, submit your assembled contigs to the RAST server or to the NCBI PGAAP server. RAST is very easy to use. You may wish to try different assemblers and submit the results from each to RAST. Then you may be able to judge which assembly is best suited for submission to NCBI.  MG-RAST is available for meta-genomic data.