Purdue University

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from sequencing reads or reference sequences. It is highly scalable in terms of the size of the input data.

Cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.

Dbg2olc is used for efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies.

Debreak is a SV caller for long-read single-molecular sequencing data.

DeconSeq: DECONtamination of SEQuence data using a modified version of BWA-SW. The DeconSeq tool can be used to automatically detect and efficiently remove sequence contamination from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.

Deepbgc is a tool for BGC detection and classification using deep learning.

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Deepsignal2 is a deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads.

DeepSpeed is a deep learning optimization library that makes distributed training easy, efficient, and effective.

DeepTools is a collection of user-friendly tools for normalization and visualization of deep-sequencing data.

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.

Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.

DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc.

Diamond is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data.

dnaapler is a simple python program that takes a single nucleotide input sequence (in FASTA format), finds the desired start gene using blastx against an amino acid sequence database, checks that the start codon of this gene is found, and if so, then reorients the chromosome to begin with this gene on the forward strand.

Dnaio is a Python 3.7+ library for very efficient parsing and writing of FASTQ and also FASTA files.

Dragonflye is a pipeline that aims to make assembling Oxford Nanopore reads quick and easy.

Drep is a python program for rapidly comparing large numbers of genomes.