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.
Whole Genome Sequencing
Spades | Well-supported and updated genome assembler.
AllPaths | If you follow the formula, it is the best.
DISCOVAR | No longer supported
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.
QIIME | A good starting point, but with limits
USEARCH | A more powerful and flexible option to QIIME
MetagenomicSeq | DESeq for metagenomics