StaPH-B

BBTools suite of tools from Joint Genome Institute

Freyja: recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset

FastQC: A quality control analysis tool for high throughput sequencing data

Plotting tool for long read sequencing data and alignments

Software package for assigning SARS-CoV-2 genome sequences to global lineages

polypolish: a tool for polishing genome assemblies with short reads

Viral Annotation DefineR: classification and annotation of viral sequences

NCBI Datasets: easily gather data from across NCBI databases

Fast genome and metagenome distance estimation using MinHash http://mash.readthedocs.org