The core methods and software around which the Ocean Genomics ecosystem is built are open source. It is our commitment that they remain open source, and freely available, and well supported.
Wicked fast expression quantification.
Salmon quantifies the level of expression of each gene and transcript in your RNA-seq sample. Each sample is quantified using an automatically learned, sample-specific bias model and each calculation comes with a measure of statistical confidence. Salmon can derive quantifications from your prebuilt alignments or using its own fast-read mapper.
Assemble novel transcripts.
Scallop identifies novel transcripts in your RNA-seq sample by performing complete transcriptome assembly. From your sample and a reference genome, Scallop identifies a set of transcripts that can explain the sequencing reads you observed, making particular use of long-range mate-pair information.
Predict structural variants from RNA-seq.
Squid finds structural variants that affect expressed gene products within your RNA-seq sample. Squid detects both fusion genes and SVs that involve previously unexpressed regions, so you are not limited to current transcript annotations.