Purdue University

Panoply is a Java-based cross-platform NetCDF, HDF and GRIB Data Viewer.

PanPhlAn (Pangenome-based Phylogenomic Analysis) is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples.

PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunities across the hardware and software stack.

NVIDIAs Clara Parabricks brings next generation sequencing to GPUs, accelerating an array of gold-standard tooling such as BWA-MEM, GATK4, Googles DeepVariant, and many more.

ParaFly provides a simple mechanism for running a predefined list of unix commands in parallel using multithreading. Failed processes are captured and reported. Successfully executed processes are noted. If the process is rerun, only those previously incompleted or failed processes will be executed.

GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input.

PnetCDF Parallel netCDF is a high-performance parallel I/O library for accessing files in format compatibility with Unidatas NetCDF, specifically the formats of CDF-1, 2, and 5.

Parallel-fastq-dump is the parallel fastq-dump wrapper.

There is no ParaView client GUI in this container, but ParaView Web application is included.

Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a region, Inversions of a region, or Translocations between two regions in the genome.

Parsnp is used to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours.

PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences.

Pbccs is a tool to generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads).

pblat is parallelized blat with multi-threads support.

Pbmm2 is a minimap2 frontend for PacBio native data formats.

pbptyper is a tool to identify the Penicillin Binding Protein (PBP) of Streptococcus pneumoniae assemblies.

PCAngsd is a program that estimates the covariance matrix and individual allele frequencies for low-depth next-generation sequencing (NGS) data in structured/heterogeneous populations using principal component analysis (PCA) to perform multiple population genetic analyses using genotype likelihoods.

Peakranger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data.

PEPPER is a genome inference module based on recurrent neural networks that enables long-read variant calling and nanopore assembly polishing in the PEPPER-Margin-DeepVariant pipeline. This pipeline enables nanopore-based variant calling with DeepVariant.