inst/scripts/README.md

In nikopech/lineagespot: Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing

lineagespot example datasets

Raw fastq analysis

Example fastq files are provided through zenodo. For the pre processing steps of them, the bioinformatics analysis pipeline is provided here.

The bioinformatics pipeline used for the analysis is based on the CDC ARTIC on Illumina Bioinformatic Workflow: https://github.com/CDCgov/SARS-CoV-2_Sequencing/tree/master/protocols/BFX-UT_ARTIC_Illumina

NC_045512.2 annotation file

The provided gene annotation file (GFF3) has been downloaded from NCBI SARS-CoV-2 resources.

Lineage reports references

The provided tab-delimited txt files containing lineage variants have been manually created based on outbreak.info reports.

nikopech/lineagespot documentation built on Dec. 28, 2021, 12:15 a.m.