For large scale analyses, use UA High Performance/High Throughput Computing systems. See the UA HTC FAQs
See the BLAST FAQ
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.
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:
To use an unsupported module, run the commands:
module load unsupported
module load group/program/version
See the FAQ HERE
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.