gencove

The Gencove CLI

What is Gencove?

Gencove is a high-throughput, cost-effective platform for genome sequencing and analysis, enabling a wide array of genomics applications across industries. Furthermore, it is the only enterprise analytics platform for low-pass whole genome sequencing (lpWGS).

The Gencove command-line interface (CLI) can be used to easily access the Gencove platform.

Main Features

It is most often used for:

• Uploading FASTQ files for analysis
• Downloading analysis results which include the following:
  • Sequence (.fastq.gz)
  • Alignment (.bam, .bai)
  • Imputation (.vcf.gz, .vcf.gz.tbi, .vcf.gz.csi)
• Assigning metadata to Gencove samples

Before filing a bug report, please refer to the following link. Bugs should be reported here.

Installation

# install via PyPI
pip install gencove

# updating to latest version
pip install -U gencove

Documentation

Online documentation (with examples) is available at docs.gencove.com

API reference for publicly available endpoints: API Reference

Comprehensive CLI Documentation available: CLI Reference