Pittsburgh Supercomputing Center's repositories
singularity-guppy-gpu
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms.
singularity-bedops
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
singularity-bismark
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
singularity-blast
BLAST finds regions of similarity between biological sequences.
singularity-bowtie2
bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
singularity-browsh
Browsh is a fully-modern text-based browser.
singularity-btop
A monitor of resources
singularity-busco
BUSCO is a tool to assess completeness of genome assembly, gene set, and transcriptome.
singularity-cwltool
The Common Workflow Language (CWL) is an open standard for describing analysis workflows and tools in a way that makes them portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments.
singularity-fdupes
FDUPES is a program for identifying or deleting duplicate files residing within specified directories.
singularity-flash
FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments.
singularity-genemark-es
Novel genomes can be analyzed by GeneMark-ES, an algorithm utilizing models parameterized by unsupervised training. Notably, GeneMark-ES has a special option for fungal genomes to account for fungal-specific intron organization.
singularity-jp
The jp command is a command line interface to JMESPath, an expression language for manipulating JSON.
singularity-ncview
ncview is a visual browser for netCDF format files.
singularity-raw2ometiff
Raw format to OME-TIFF converter.
singularity-raxml
RAxML - Randomized Axelerated Maximum Likelihood.
singularity-salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
singularity-samtools
Samtools is a suite of programs for interacting with high-throughput sequencing data.
singularity-shellcheck
ShellCheck, a static analysis tool for shell scripts
singularity-tiger
Target/Integrative Genetic Element Retriever
singularity-viennarna
The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.