Bioinformatics

The page is populated with links to programs that we commonly use in the lab for analyzing our next-generation sequencing datasets. If you are interested in having us run, whole genome or transcriptomes for you on our fee-based computer cluster, please do not hesistate to contact us. The fees are quite reasonable.

If you are just getting started, you should look into paid programs like CLC Genomics Workbench or Geneious Pro, or GALAXY which is open source.

Whole Genome Sequencing
Spades | Well-supported and updated genome assembler.
AllPaths | If you follow the formula, it is the best.
DISCOVAR | No longer supported

Transcriptomics
Trinity | Our favorite de novo transcriptome assembler for RNAseq data. It has lots of capabilities, but does have significant memory requirements.
DESeq | Our program of choice for identifying differentially expressed gene transcripts. It is one of the few programs that can handle multiple factors and uses GLM frameworks.

16s Metagenomics
QIIME | A good starting point, but with limits
USEARCH | A more powerful and flexible option to QIIME
MetagenomicSeq | DESeq for metagenomics