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Fit population genetic models using diffusion approximations to the allele frequency spectrum

An automated pipeline for processing DamID sequencing datasets

Recovery of genomes from metagenomes via a dereplication,

A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. It provides two models,deepARG-SS and deepARG-LS.

A set of user-friendly tools for normalization and visualzation of deep-sequencing data

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data

Structural variant discovery by integrated paired-end and split-read analysis

a collaborative endeavour to develop new diffraction integration software to meet the data analysis requirements presented by these recent advances

Accelerated BLAST compatible local sequence aligner

DISCASM aims to extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads. DISCASM relies on the output from STAR (as run via STAR-Fusion), and supports de novo transcriptome assembly using Trinity or Oases. - https://github.com/DISCASM/DISCASM/wiki

Designed for discovering all kinds of SNPs

an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features

DockingApp is a user-friendly graphical application for carrying out molecular docking and virtual screening tasks, meant to enable non-experienced users to easily perform such activities and browse the docking results via a three-dimensional visualization.

Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

Dragmap is the Dragen mapper/aligner Open Source Software.

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

De-replication of microbial genomes assembled from multiple samples

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab

high-performance compression of sequencing reads stored in FASTQ format

Dynamo is a software environment for subtomogram averaging of cryo-EM data