Seqpipe

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Welcome!

Seqpipe Ltd provides software consulting services. Our mission is to help life science practitioners dealing with large amounts of next-generation sequencing data

We help bioinformaticians to productionize their newly developed algorithms and pipelines and to turn them into easy to use and scalable bioinformatics tools and applications.

Seqpipe has a team of software engineers and bioinformaticians who can apply software engineering best practices for development of bioinformatics software

Seqpipe consult and implement parallelization of bioinformatics algorithms and pipelines on top of various cluster management systems and GPUs. We consult usage of big data tools (Apache Hadoop, Apache Spark, Apache Impala, etc) in development of bioinformatics applications and pipelines.

Projects

Showcasing our work

GPF - Genotypes and Phenotypes in Families

GPF - Genotypes and Phenotypes in Families

Overview

The Genotype and Phenotype in Families (GPF) system manages large databases of genetic variants and phenotypic measurements obtained from large collections of families and individual family members.

Responsibilities

Software developemnt, maintenence, deployment and system administration of the system.

Tools & Technologies

Python, numpy, pandas, scipy, matplotlib, pyarrow, statsmodels, cyvcf2, pysam, samtools, Django, Angular, Apache Hadoop, Apache Impala

More information

Github project page

s-GAINS

s-GAINS: Sparse Genomic Analysis of Individual Nuclei by Sequencing

Overview

Integrates all steps of the single-cell CNV profiling computational pipeline from aligning NGS reads to preparation of the the data for visualization and analysis into a single tool.

Responsibilities

Software design, developemnt, maintenence, packaging and distribution of the tool.

Tools & Technologies

Python, numpy, pandas, scipy, pysam, biopython, bowtie, samtools

More information

Github project page

SCclust

SCclust - Segmentation and Clustering of Single Cell Sequencing Copy Number Profiles

Overview

The SCclust package implements feature selection based on breakpoints, permutations for FDRs for Fisher test p-values and identification of the clone structure in single cell copy number profiles.

Responsibilities
  • Software design, developemnt, maintenence, packaging and distribution of the tool.
Tools & Technologies

R, Bioconductor DNAcopy.

More information

Github project page

SCGV

SCGV - Single Cell Genome Viewer

Overview

SCGV is an interactive graphical tool for single-cell genomics data, with emphasis on single-cell genomics of cancer. It facilitates examination, jointly or individually, of DNA copy number profiles of cells harvested from multiple anatomic locations (sectors)

Responsibilities
  • Software design, developemnt, maintenence, packaging and distribution of the tool.
Tools & Technologies

Python, numpy, pandas, matplotlib, PyQt

More information

Github project page

Contacts

Get in touch:

We'd love to get a note from you!

E-mail

info [at] seqpipe [dot] com

Telephone

00 359 889 725 503