Purdue University

Pybigwig is a python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.

Pychopper is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.

Pycoqc is a tool that computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.

Pyensembl is a Python interface to Ensembl reference genome metadata such as exons and transcripts.

Pyfaidx is a Python package for random access and indexing of fasta files.

pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable.

pyGenomeViz is a genome visualization python package for comparative genomics implemented based on matplotlib.

Pyranges are collections of intervals that support comparison operations (like overlap and intersect) and other methods that are useful for genomic analyses.

Pysam is a python module that makes it easy to read and manipulate mapped short read sequence data stored in SAM/BAM files.

Native Python 3.9.5 including optimized libraries.

PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.

PyVCF3 has been created because the Official PyVCF repository is no longer maintained and do not accept any pull requests.

QEMU is a generic and open source machine emulator and virtualizer.

QIIME 2 is a is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency. QIIME 2 enables researchers to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical results.

QMCPACK is an open-source, high-performance electronic structure code that implements numerous Quantum Monte Carlo algorithms. Its main applications are electronic structure calculations of molecular, periodic 2D and periodic 3D solid-state systems.

Qt is a comprehensive cross-platform C++ application framework.

Bulked segregant analysis, as implemented in QTL-seq (Takagi et al., 2013), is a powerful and efficient method to identify agronomically important loci in crop plants. QTL-seq was adapted from MutMap to identify quantitative trait loci. It utilizes sequences pooled from two segregating progeny populations with extreme opposite traits (e.g. resistant vs susceptible) and a single whole-genome resequencing of either of the parental cultivars.

Qualimap is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.

Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale based on density-functional theory, plane waves, and pseudopotentials.