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.

Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.

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

De novo metazoan mitochondrial genome annotation.

Consensus module for raw de novo DNA assembly of long uncorrected reads Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.

a de novo genome assembler for long reads. Raven is a de novo genome assembler for long uncorrected reads.

Efficient and comprehensive structural variant caller for massive parallel sequencing data. Identify chromosomal rearrangements using Mate Pair or Paired End sequencing data. It allows identification of intra and inter-chromosomal translocations, deletions, tandem-duplications and inversions, using supplementary alignments as well as discordant pairs.

Scripts for parsing Mykrobe predict results for Shigella sonnei.