# Benchling Acquires PipeBio

**Benchling has acquired PipeBio!** [Learn more](https://pipebio.com/blog/pipebio-joins-benchling)

## Antibody discovery

### Identify antibody liabilities and PTMs
De-risk antibody development by identifying sequence liabilities and flagging sequence motifs of residues that may give rise to PTMs and affect the structure and function antibody candidates.

### Antibody hit expansion and data mining
Use PipeBio for mining NGS repertoires for expanding potential hit sequences of characterized antibody sequences.

## NGS analysis

### Analyze NGS from antibody library, repertoire sequencing and panning
Annotate and cluster NGS data from biopanning experiments and find differentially enriched sequence clusters across multiple panning rounds.

### Identify enriched and diverse antibodies with good binding properties
Add functional assay data, such as ELISA, FACS and other immunoassay data and use built-in tools to identify the most diverse antibodies for synthetization and characterization.

## Sanger sequences

### Easy Sanger analysis
Trim, assemble forward and reverse reads, detect heterozygous peaks, annotate, edit and align Sanger sequences.

## Antibody engineering

### Calculate protein properties and show hydrophobic regions
Use built-in tools to calculate charge, isoelectric point (pI), molecular weight and identify hydrophobic regions in your antibody or peptide sequences.

### Predict antibody structure
Predict antibody (VH-VH from IgG) or nanobody (VHH) structures and obtain .PDB files for predicted structures.

### Sequence editing, codon optimization
Bulk clone many insert fragments in one simple operation, Identify problematic internal cut sites, edit your sequences in-line in the editor, export to excel, genbank, QPIX.

## Scientists

### Tools for easy sequence analysis and visualization
PipeBio has a simple user interface and easy-to-use tools to analyze and visualize your antibody sequences.

## Bioinformaticians

### Integrate, build automated workflows and manage data
Use PipeBio's flexible tools, scalable compute and data storage capabilities to build and optimize workflows.

## Tools for sequence analysis

### Accurate Annotation Engine
- Identify and correct truncated framework regions
- Detect frame shifts
- Flag liabilities defined by your preferences as errors and warnings
- Flexible support for numbering schemes and annotation definitions, including IMGT, Kabat, Chothia

### IgG, VHH, scFv, BCR and TCR sequence analysis
- Flexible support for IgG, Fab, Nanobody (VHH), linkers for ADCs, affibodies
- Both for synthetic libraries and naturally occurring sequences.
- Annotate CDRs, FRs, V-gene, J-gene, C-gene, α-chain, β-chain, VH, VL
- BCR and TCR repertoire sequencing analysis

### Custom Germline Database
- Annotate sequence with any germline, including llama, mouse, rabbit, rat, canine, human and more
- Works just as well on synthetic libraries and naturally occurring sequences
- Flexible support for numbering schemes and annotation definitions, including IMGT, Kabat, Chothia

### Cluster & Compare sequences
- Define your clonotype by cluster on germline, FR, CDR-H or CDR-L, C-regions or across entire VH and VL chains
- Examine sequence diversity in samples and individual clusters
- Dive deeper inside interesting clusters and clonotypes
- Compare samples with tens of millions of sequences from antibody repertoire sequencing, biopanning, phage display

### Visualize phylogeny, clusters, enrichment, frequencies and more
- Use the phylogenetic tree to visualize antibody clonotypes with functional assay data to find ideal sequences
- Use interactive charts to quickly find sequences by specific residues in certain positions, relevant clusters and more

### Fast NGS and Sanger sequence analysis
Highly parallelized cloud computing allows you to get results, fast:
- Analyze billions of sequences (up to NovaSeq) in a couple of days
- Tens of millions of NGS reads in hours
- Hundreds of thousands of NGS reads in minutes
- Hundreds of Sanger sequences in minutes

### Supported sequences and file formats
- Analyze data from Illumina (NovaSeq, NextSeq, MiSeq, iSeq)
- 10x Genomics single-cell sequencing support
- PacBio and soon Oxford Nanopore
- Supported file formats range from Ab1, Fastq, Fasta, Genbank to CSV and Excel (both import and export)

### The integrated cloud software for antibody sequence analysis
[Get started for free](https://pipebio.com/sign-up)