Canary: an atomic pipeline for clinical amplicon assays.

ABSTRACT:

Background

High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number of shortcomings: they lack robustness and have many components written in multiple languages, each with a variety of resource requirements. Pipeline components must be linked together with a workflow system to achieve the processing of FASTQ files through to a VCF file of variants. Crafting these pipelines requires considerable bioinformatics and IT skills beyond the reach of many clinical laboratories.

Results

Here we present Canary, a single program that can be run on a laptop, which takes FASTQ files from amplicon assays through to an annotated VCF file re

SUBMITTER: Doig KD 

PROVIDER: S-EPMC5732437 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature