Add new workflow reconstruct_from_alignments which uses a new tool (reconstructR) to infer disease transmission links based on genomic (consensus genome and intrahost variation) data.
The input to this workflow includes an aligned/trimmed BAM and consensus genome (FASTA) per disease case, plus a single reference genome (FASTA, the same one the BAM files are already aligned against). This workflow will perform the necessary intrahost variant calling, multiple alignments, etc, and produce output per the reconstructR tool.
Add new workflow
reconstruct_from_alignmentswhich uses a new tool (reconstructR) to infer disease transmission links based on genomic (consensus genome and intrahost variation) data.The input to this workflow includes an aligned/trimmed BAM and consensus genome (FASTA) per disease case, plus a single reference genome (FASTA, the same one the BAM files are already aligned against). This workflow will perform the necessary intrahost variant calling, multiple alignments, etc, and produce output per the reconstructR tool.