Our Applications

Salmon

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.

 

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Salmon

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.

 

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Kourami

Kourami extracts HLA alleles from DNA sequencing.

It will identify the closest known HLA alleles matching your sample and provide a standard typing result. It will also assemble and report novel alleles if they are present in your sample.

 

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Kourami

Kourami extracts HLA alleles from DNA sequencing.

It will identify the closest known HLA alleles matching your sample and provide a standard typing result. It will also assemble and report novel alleles if they are present in your sample.

 

Version now availableDownload Now

Scallop

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.

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Scallop

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.

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Squid

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.

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Squid

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.

Version now availableDownload Now

Our Commitment

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.

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