Year in review

The PipeBio platform has seen a bunch of development during 2022 which have been well received by our customers. We've come forth with many new features and tools for NGS analysis and Sanger analysis, including tools for visualization and efficient analysis. We picked a few features released during this year for this article.

Scaling analysis up to NovaSeq

We wrote about how to analyze billions of NGS sequences earlier this year, which marks a milestone for a next level of scalable NGS analysis on the PipeBio platform. We’re able to scale up to sequence analysis billions of reads and now have customers routinely analyzing sequences from NovaSeq runs (in a couple of days).

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Improved annotation

We recently released our new and improved annotation tool. It is now even more accurate being able to detect germline mutations on the nucleotide level as well as define region boundaries and frameshift locations with greater accuracy. As before, our annotation engine supports multiple numbering schemes (IMGT, Kabat, AbM, custom), a variety of species from Human, Alpaca, Llama, Rabbit, Chicken to any custom germline gene databases.

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Annotation of nucleotide and amino acid mutations from germline genes on PipeBio — Nucleotide mutations from germline annotated

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SSO & SCIM

Earlier this year we rolled out support for SSO and SCIM on PipeBio for enterprise customers. SSO allows easy management of access control and employee sign-on activities, which is a requirement for many companies. SCIM again allows automation of user identity management across IT systems and is also supported by PipeBio. Implementation of PipeBio’s SSO and SCIM is straightforward and well-documented.

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Logos of some of the supported SSO and SCIM providers for PipeBio — Some of the supported SSO and SCIM providers

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Phylogenetic tree

This year we introduced the phylogenetic tree chart that enables visualization of both sequence alignments and associated metadata, such as ELISA and binding assays. You can use the tree as a flexible tool to visualize the diversity of your antibodies or peptides, clonal families as well as hit pick sequences based on liabilities or developability visually.

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A radial view of a phylogenetic tree of antibody sequences on PipeBio — A radial view of the phylogenetic tree

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Cluster view

The cluster view chart is a precursor to our up and coming charts for better visualizing relationships between sequences and clonal families. We also showed how to use the chart to visualize an immune repertoire from tonsil immune cells, Ig isotypes and B cell stages (naive B cell, Germinal Center, Memory B cell and Plasmablasts) in our article on analyzing single B cell repertoires and 10x Genomics barcoded data.

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Hydrophobic regions and protein properties

We implemented coloring and numerical representations of hydrophobic patches for all sequences. We also implemented a tool for calculation of sequence protein properties (such as charge, molecular weight etc.) for sequences. You can find more information about hydrophobicity and protein properties on our website.

Hydrophobicity analysis of antibody sequences and calculation of molecular weight, isoelectric point, extinction coefficient, charge and aliphatic index on PipeBio — Hydrophobic regions colored in sequence viewer and the dialogue for calculating protein properties of sequences

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New website

We are proud to have released the newest iteration of our website with a fresh look, better navigation and updated content. If you’re reading this blog post, congratulations, you’re already on our new website.

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