Pittsburgh Supercomputing Center's repositories
singularity-bamtools
C++ API & command-line toolkit for working with BAM data
singularity-bcftools
bcftools — utilities for variant calling and manipulating VCFs and BCFs.
singularity-cutadapt
cutadapt removes adapter sequences from sequencing reads.
singularity-deephyperx
A Python tool to perform deep learning experiments on various hyperspectral datasets.
singularity-fastani
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)
singularity-fastx-toolkit
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
singularity-flac
FLAC (/flæk/; Free Lossless Audio Codec) is an audio coding format for lossless compression of digital audio.
singularity-hisat2
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.
singularity-htslib
HTSlib A C library for reading/writing high-throughput sequencing data.
singularity-kraken2
Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds.
singularity-methylpy
METHYLPY, is an analysis pipeline for DNA methylation data.
singularity-phylip-suite
PHYLIP is a free package of programs for inferring phylogenies.
singularity-picard
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
singularity-prodigal
Fast, reliable protein-coding gene prediction for prokaryotic genomes.
singularity-prokka
Prokka: rapid prokaryotic genome annotation.
singularity-sra-toolkit
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
singularity-trimmomatic
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data