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singularity-fastx-toolkit

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

singularity-fdupes

FDUPES is a program for identifying or deleting duplicate files residing within specified directories.

singularity-ffmpeg

A complete, cross-platform solution to record, convert and stream audio and video.

singularity-flac

FLAC (/flæk/; Free Lossless Audio Codec) is an audio coding format for lossless compression of digital audio.

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-funannotate

Eukaryotic Genome Annotation Pipeline

singularity-gatk

The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data.

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-gent

This program computes the cross entropy for groups of sequences that have been assigned to groups on the basis of biochemical, physiological, or other biological property.

singularity-glances

Glances is a cross-platform system monitoring tool written in Python.

singularity-gnuplot

Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.

singularity-graphviz

Graphviz is a package of open-source tools initiated by AT&T Labs Research for drawing graphs specified in DOT language scripts.

singularity-guppy

Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms.

singularity-guppy-gpu

Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms.

singularity-hashdeep

md5deep is a set of programs to compute MD5, SHA-1, SHA-256, Tiger, or Whirlpool message digests on an arbitrary number of files.

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-hmmer

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

singularity-homer

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

singularity-htslib

HTSlib A C library for reading/writing high-throughput sequencing data.

singularity-hyperfine

A command-line benchmarking tool.

singularity-imagemagick

Use ImageMagick® to create, edit, compose, or convert digital images.

singularity-infernal

singularity-jp

The jp command is a command line interface to JMESPath, an expression language for manipulating JSON.

singularity-jq

jq is a lightweight and flexible command-line JSON processor.

singularity-kakoune

Kakoune is a code editor heavily inspired by Vim.

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-lazygit

Simple terminal UI for git commands

singularity-libtiff-tools

A small collection of programs for converting non-TIFF format images to TIFF and for manipulating and interogating the contents of TIFF images.

singularity-lowcharts

lowcharts is meant to be used in those scenarios where we have numerical data in text files that we want to display in the terminal to do a basic analysis.

singularity-mc

GNU Midnight Commander is a visual file manager, licensed under GNU General Public License and therefore qualifies as Free Software.