HDF4 also known as HDF is a library and multi-object file format for storing and managing data between machines.

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

HELEN is a multi-task RNN polisher which operates on images produced by MarginPolish.

Hicpro is an optimized and flexible pipeline for Hi-C data processing.

Hicexplorer is a set of tools to process, normalize and visualize Hi-C data.

Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads.

HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome.

Hmmer is used for searching sequence databases for sequence homologs, and for making sequence alignments.

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.

Homopolish is a genome polisher originally developed for Nanopore and subsequently extended for PacBio CLR. It generates a high-quality genome (>Q50) for virus, bacteria, and fungus. Nanopore/PacBio systematic errors are corrected by retreiving homologs from closely-related genomes and polished by an SVM.

How_are_we_stranded_here is a python package for testing strandedness of RNA-Seq fastq files.

HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nations largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a programs work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur.

Install HSI/HTAR using the Cygwin installer.

Hspice is a device level circuit simulator. Hspice takes a spice file as input and produces output describing the requested simulation of the circuit. It can also produce output files to be used by the AWAVES post processor.

The HTAR program manipulates HPSS-resident archives, or archives that reside on a remote system (subject to the restrictions noted below), by writing files to, or retrieving files from, either HPSS or a remote FTP server.

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

Htslib is a C library for high-throughput sequencing data formats.

Htstream is a quality control and processing pipeline for High Throughput Sequencing data.

HUMAnN 3.0 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network. HUMAnN is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.

The Hardware Locality hwloc software project.