Whole genome sequencing Tools

DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.

Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

De novo metazoan mitochondrial genome annotation.

Scripts for parsing Mykrobe predict results for Shigella sonnei.