A SARS-CoV-2 genome reconstruction and SNV calling tool from metagenomic and metatranscriptomic sequencing data.
Three pipelines exist:
Construct contig sequences from Illumina paired-end fastq files.
Consensus sequence generation and SNV calling from Illumina paired-end fastq files.
Consensus sequence generation and SNV calling from Oxford Nanopore fast5 and fastp files.
All of three pipeline can be used in NIG supercomputer https://sc.ddbj.nig.ac.jp/en?set_language=en