Biology subjects

Marriott, H.

Publications and source records attributed to Marriott, H..

3 recordsLinked to original sources

bioRxiv2022

DNAscan2: a versatile, scalable, and user-friendly analysis pipeline for next-generation sequencing data

The current widespread adoption of next-generation sequencing (NGS) in all branches of basic and clinical genetics fields means that users with highly variable informatics skills, computing facilities and application purposes need to process, analyse, and interpret NGS data. In this landscape, versatility, scalability, and user-friendliness are key characteristics for an NGS analysis tool. We developed DNAscan2, a highly flexible, end-to-end pipeline for the analysis of NGS data, which (i) can be used for the detection of multiple variant types, including SNVs, small indels, transposable elements, short tandem repeats and other large structural variants; (ii) covers all steps of the analysis, from quality control of raw data to the generation of html reports for the interpretation and prioritisation of results; (iii) is highly adaptable and scalable as it can be deployed and run via either a graphic user interface for non-bioinformaticians, a command line tool for personal computer usage, or as a Snakemake workflow that facilitates parallel multi-sample execution for high-performance computing environments; (iv) is computationally efficient by minimising RAM and CPU time requirements. Availability and ImplementationDNAscan2 is implemented in Python3 and is available to download as a command-line tool and graphical-user interface at https://github.com/KHP-Informatics/DNAscanv2 or a Snakemake workflow at https://github.com/KHP-Informatics/DNAscanv2_snakemake.

bioinformatics↗

bioRxiv2022

RetroSnake: a Modular End-to-End Pipeline for Detection of Human Endogenous Retrovirus (HERV) Transposable Elements in Next Generation Sequencing (NGS) Data

Human Endogenous Retroviruses (HERVs) integrated into the genome of vertebrates as a result of ancient exogenous infections and currently comprise [~]8% of our genome. The majority of these elements have accumulated mutations rendering them inactive. The most recently acquired members, HERV-K have potential to produce viral particles and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV discovery exist, most of them lack wet-lab validation of their results and are not end-to-end as they do not cover all steps of the analysis. These factors greatly limit their use. Here we describe RetroSnake, an end-to-end, modular, computationally efficient and customisable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake presents important advantages with respect to other available tools. For instance, it is the only pipeline based on an extensively wet-lab validated protocol, and it is the most complete transposable elements detection pipeline, producing annotated insertions presented as an interactive html file, easy enough to use by life scientists without substantial computational training. Availability and implementationThe Pipeline and an extensive documentation are available at https://github.com/KHP-Informatics/RetroSnake Contactalfredo.iacoangeli@kcl.ac.uk

genomics↗

bioRxiv2017

Nanopore sequencing and assembly of a human genome with ultra-long reads

Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation. However until recently nanopore sequencing has been mainly applied to small genomes, due to the limited output attainable. We present nanopore sequencing and assembly of the GM12878 Utah/Ceph human reference genome generated using the Oxford Nanopore MinION and R9.4 version chemistry. We generated 91.2 Gb of sequence data ([~]30x theoretical coverage) from 39 flowcells. De novo assembly yielded a highly complete and contiguous assembly (NG50 [~]3Mb). We observed considerable variability in homopolymeric tract resolution between different basecallers. The data permitted sensitive detection of both large structural variants and epigenetic modifications. Further we developed a new approach exploiting the long-read capability of this system and found that adding an additional 5x-coverage of ultra-long reads (read N50 of 99.7kb) more than doubled the assembly contiguity. Modelling the repeat structure of the human genome predicts extraordinarily contiguous assemblies may be possible using nanopore reads alone. Portable de novo sequencing of human genomes may be important for rapid point-of-care diagnosis of rare genetic diseases and cancer, and monitoring of cancer progression. The complete dataset including raw signal is available as an Amazon Web Services Open Dataset at: https://github.com/nanopore-wgs-consortium/NA12878.

genomics↗