A modified version of the ashure ASHURE analysis tool, designed to identify Sars-covid-19 variants in Waste-water.
This repository is under development and not ready for public use
The use of nanopore sequencing with its rapid sequencing make it ideal for testing waste-water for the presence of covid-variants (and other pathogens). However the sequencing accuracy remains a significant issue when calling variants. Here we leverage RCA to error correct nanopore sequencing error for ARTIC amplicons using a modified version of ASHURE developed by https://github.com/BBaloglu/ASHURE. Please read and cite ASHURE for more information.
1: Alignment against ARTIC covid amplicons to identify and label fragments.
2: Running per sequence, cut out repeats (in memory) and generate consesus, outputting to a csv.
3: Filter out consensus with fewer than 10 repeats and outside minimum expected amplicon length.
4: Clustering?
4: Convert to Fasta and map to covid genome with STAR.
singularity build --remote ncov-ashure.sif Singularity.recipe
singularity run ncov-ashure.sif -i data.fastq
Read our paper here: https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/2041-210X.13561
If you use ASHURE in your work, please cite:
Baloğlu, B., Chen, Z., Elbrecht, V., Braukmann, T., MacDonald, S. and Steinke, D. (2021). A workflow for accurate metabarcoding using nanopore MinION sequencing. Methods Ecol Evol. 2021;12:794– 804. https://doi.org/10.1111/2041-210X.13561
Baloğlu, B. & Chen, Z. (2021). ASHURE. Version 1.0.0. Zenodo. DOI: 10.5281/zenodo.4450611