Purdue University

Drop-seq are java tools for analyzing Drop-seq data.

Dropest is a pipeline for initial analysis of droplet-based single-cell RNA-seq data.

Dsuite is a fast C++ implementation, allowing genome scale calculations of the D and f4-ratio statistics across all combinations of tens or hundreds of populations or species directly from a variant call format (VCF) file.

easySFS is a tool for the effective selection of population size projection for construction of the site frequency spectrum.

Edta is is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries.

Eggnog-mapper is a tool for fast functional annotation of novel sequences.

Eigen is a C++ template library for linear algebra matrices, vectors, numerical solvers, and related algorithms.

The Emacs programmable text editor.

Emboss is The European Molecular Biology Open Software Suite.

Ensembl-vep (Ensembl Variant Effect Predictor) predicts the functional effects of genomic variants.

ENVI is the premier software solution for processing and analyzing geospatial imagery used by scientists, researchers, image analysts, and GIS professionals around the world.

Epic2 is an ultraperformant Chip-Seq broad domain finder based on SICER.

Evidencemodeler is a software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures.

Exonerate is a generic tool for pairwise sequence comparison/alignment.

Expansion Hunter: a tool for estimating repeat sizes.

Fasta3 is a suite of programs for searching nucleotide or protein databases with a query sequence.

FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).

Fastp is an ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging, etc).

Fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format.

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.