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Modules

Franklin currently uses lmod, which is cross-compatible with envmod. See our lmod docuementation for more information on using the module system.

Organization

Many modules correspond to different versions of the same software, and some software has multiple variants of the same version. The default naming convention is NAME/VERSION: for example, cuda/11.8.0 or mcl/14-137. The version can be omitted when loading, in which case the highest-versioned module or the version marked as default (with a (D)) will be used.

Variants

Some module names are structured as NAME/VARIANT/VERSION. For these, the minimum name you can use for loading is NAME/VARIANT: for example, you can load relion/gpu or relion/cpu, but just trying to module load relion will fail.

Architectures

Software is sometimes compiled with optimizations specific to certain hardware. These are named with the format NAME/VERSION+ARCH or NAME/VARIANT/VERSION+arch. For example, ctffind/4.1.14+amd was compiled with AMD Zen2-specific optimizations and uses the amdfftw implementation of the FFTW library, and will fail on the Intel-based RTX2080 nodes purchased by the Al-Bassam lab (gpu-9-[10,18,26]). Conversely, ctffind/4.1.14+intel was compiled with Intel-specific compiler optimizations as well as linking against the Intel OneAPI MKL implementation of FFTW, and is only meant to be used on those nodes. In all cases, the +amd variant of a module, if it exists, is the default, as the majority of the nodes use AMD CPUs.

Software without a +ARCH was compiled for a generic architecture and will function on all nodes. The generic architecture on Franklin is x86-64-v3, which means they support AVX, AVX2, and all other previous SSE and other vectorized instructions.

Conda Environments

The various conda modules have their own naming scheme. These are of the form conda/ENVIRONMENT/VERSION. The conda/base/VERSION module(s) load the base conda environment and set the appropriate variables to use the conda activate and deactivate commands, while the the modules for the other environments first load conda/base and then activate the environment to which they correspond. The the conda section for more information on conda and Python on Franklin.

Spack-managed Modules

These modules are built and managed by our Spack deployment. Most were compiled for generic architecture, meaning they can run on any node, but some are Intel or AMD specific, and some require GPU support.

R

R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

Versions: 4.1.1

Arches: generic

Modules: R/4.1.1

abyss

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size.

Versions: 2.3.1

Arches: generic

Modules: abyss/2.3.1

amdfftw

FFTW (AMD Optimized version) is a comprehensive collection of fast C routines for computing the Discrete Fourier Transform (DFT) and various special cases thereof. It is an open-source implementation of the Fast Fourier transform algorithm. It can compute transforms of real and complex-values arrays of arbitrary size and dimension. AMD Optimized FFTW is the optimized FFTW implementation targeted for AMD CPUs. For single precision build, please use precision value as float. Example : spack install amdfftw precision=float

Versions: 3.2

Arches: amd

Modules: amdfftw/3.2+amd

ant

Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other

Versions: 1.10.7

Arches: generic

Modules: ant/1.10.7

aragorn

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.

Versions: 1.2.38

Arches: generic

Modules: aragorn/1.2.38

bedtools2

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.

Versions: 2.30.0

Arches: generic

Modules: bedtools2/2.30.0

blast-plus

Basic Local Alignment Search Tool.

Versions: 2.12.0

Arches: generic

Modules: blast-plus/2.12.0

blast2go

Blast2GO is a bioinformatics platform for high-quality functional annotation and analysis of genomic datasets.

Versions: 5.2.5

Arches: generic

Modules: blast2go/5.2.5

blat

BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm.

Versions: 35

Arches: generic

Modules: blat/35

bowtie

Bowtie is an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers.

Versions: 1.3.0

Arches: generic

Modules: bowtie/1.3.0

bowtie2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

Versions: 2.4.2

Arches: generic

Modules: bowtie2/2.4.2

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.

Versions: 0.7.17

Arches: generic

Modules: bwa/0.7.17

bwtool

bwtool is a command-line utility for bigWig files.

Versions: 1.0

Arches: generic

Modules: bwtool/1.0

canu

A single molecule sequence assembler for genomes large and small.

Versions: 2.2

Arches: generic

Modules: canu/2.2

cap3

CAP3 is DNA Sequence Assembly Program

Versions: 2015-02-11

Arches: generic

Modules: cap3/2015-02-11

clustal-omega

Clustal Omega: the last alignment program you'll ever need.

Versions: 1.2.4

Arches: generic

Modules: clustal-omega/1.2.4

clustalw

Multiple alignment of nucleic acid and protein sequences.

Versions: 2.1

Arches: generic

Modules: clustalw/2.1

corset

Corset is a command-line software program to go from a de novo transcriptome assembly to gene-level counts.

Versions: 1.09

Arches: generic

Modules: corset/1.09

ctffind

Fast and accurate defocus estimation from electron micrographs.

Versions: 4.1.14

Arches: amd, intel

Modules: ctffind/4.1.14+intel, ctffind/4.1.14+amd

cuda

CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). Note: This package does not currently install the drivers necessary to run CUDA. These will need to be installed manually. See: https://docs.nvidia.com/cuda/ for details.

Versions: 11.8.0, 11.7.1

Arches: generic

Modules: cuda/11.8.0, cuda/11.7.1

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

Versions: 2.2.1

Arches: generic

Modules: cufflinks/2.2.1

ea-utils

Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

Versions: 2021-10-20

Arches: generic

Modules: ea-utils/2021-10-20

emboss

EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community

Versions: 6.6.0

Arches: generic

Modules: emboss/6.6.0

exonerate

Pairwise sequence alignment of DNA and proteins

Versions: 2.4.0

Arches: generic

Modules: exonerate/2.4.0

exonerate-gff3

This is an exonerate fork with added gff3 support. Original website with user guides: http://www.ebi.ac.uk/~guy/exonerate/

Versions: 2.3.0

Arches: generic

Modules: exonerate-gff3/2.3.0

fastqc

A quality control tool for high throughput sequence data.

Versions: 0.11.9

Arches: generic

Modules: fastqc/0.11.9

fftw

FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.

Versions: 3.3.10

Arches: generic

Modules: fftw/3.3.10

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Versions: 1.3.6

Arches: generic

Modules: freebayes/1.3.6

gatk

Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data

Versions: 3.8.1, 4.2.6.1

Arches: generic

Modules: gatk/3.8.1, gatk/4.2.6.1

gcc

The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, and Go, as well as libraries for these languages.

Versions: 7.5.0, 4.9.4, 5.5.0

Arches: generic

Modules: gcc/5.5.0, gcc/7.5.0, gcc/4.9.4

gctf

a GPU accelerated program for Real-Time CTF determination, refinement, evaluation and correction.

Versions: 1.06

Arches: generic

Modules: gctf/1.06

genrich

Genrich is a peak-caller for genomic enrichment assays.

Versions: 0.6

Arches: generic

Modules: genrich/0.6

ghostscript

An interpreter for the PostScript language and for PDF.

Versions: 9.56.1

Arches: generic

Modules: ghostscript/9.56.1

glimmer

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.

Versions: 3.02b

Arches: generic

Modules: glimmer/3.02b

hdf5

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.

Versions: 1.12.2

Arches: generic

Modules: hdf5/1.12.2

hisat2

HISAT2 is a fast and sensitive alignment program for mapping next- generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as against a single reference genome).

Versions: 2.2.0

Arches: generic

Modules: hisat2/2.2.0

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).

Versions: 3.3.2

Arches: generic

Modules: hmmer/3.3.2

homer

Software for motif discovery and next generation sequencing analysis

Versions: 4.9.1

Arches: generic

Modules: homer/4.9.1

hwloc

The Hardware Locality (hwloc) software project. The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.

Versions: 2.8.0

Arches: generic

Modules: hwloc/2.8.0

igv

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

Versions: 2.12.3

Arches: generic

Modules: igv/2.12.3

infernal

Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).

Versions: 1.1.4

Arches: generic

Modules: infernal/1.1.4

intel-oneapi-compilers

Intel oneAPI Compilers. Includes: icc, icpc, ifort, icx, icpx, ifx, and dpcpp. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at https://intel.ly/393CijO.

Versions: 2022.2.1

Arches: generic

Modules: intel-oneapi-compilers/2022.2.1

intel-oneapi-mkl

Intel oneAPI Math Kernel Library (Intel oneMKL; formerly Intel Math Kernel Library or Intel MKL), is a library of optimized math routines for science, engineering, and financial applications. Core math functions include BLAS, LAPACK, ScaLAPACK, sparse solvers, fast Fourier transforms, and vector math. LICENSE INFORMATION: By downloading and using this software, you agree to the terms and conditions of the software license agreements at https://intel.ly/393CijO.

Versions: 2022.2.1

Arches: generic

Modules: intel-oneapi-mkl/2022.2.1

interproscan

InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.

Versions: 5.56-89.0

Arches: generic

Modules: interproscan/5.56-89.0

iq-tree

IQ-TREE Efficient software for phylogenomic inference

Versions: 2.1.3

Arches: generic

Modules: iq-tree/2.1.3

iqtree2

Efficient and versatile phylogenomic software by maximum likelihood

Versions: 2.1.2

Arches: generic

Modules: iqtree2/2.1.2

jdk

The Java Development Kit (JDK) released by Oracle Corporation in the form of a binary product aimed at Java developers. Includes a complete JRE plus tools for developing, debugging, and monitoring Java applications.

Versions: 17.0.1

Arches: generic

Modules: jdk/17.0.1

jellyfish

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.

Versions: 1.1.11

Arches: generic

Modules: jellyfish/1.1.11

kalign

A fast multiple sequence alignment program for biological sequences.

Versions: 3.3.1

Arches: generic

Modules: kalign/3.3.1

kallisto

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.

Versions: 0.48.0

Arches: generic

Modules: kallisto/0.48.0

kmergenie

KmerGenie estimates the best k-mer length for genome de novo assembly.

Versions: 1.7044

Arches: generic

Modules: kmergenie/1.7044

kraken

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

Versions: 1.0

Arches: generic

Modules: kraken/1.0

kraken2

Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.

Versions: 2.1.2

Arches: generic

Modules: kraken2/2.1.2

krakenuniq

Metagenomics classifier with unique k-mer counting for more specific results.

Versions: 0.7.3

Arches: generic

Modules: krakenuniq/0.7.3

last

LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads).

Versions: 1282

Arches: generic

Modules: last/1282

libevent

The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

Versions: 2.1.12

Arches: generic

Modules: libevent/2.1.12

mash

Fast genome and metagenome distance estimation using MinHash.

Versions: 2.3

Arches: generic

Modules: mash/2.3

masurca

MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches.

Versions: 4.0.9

Arches: generic

Modules: masurca/4.0.9

mcl

The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

Versions: 14-137

Arches: generic

Modules: mcl/14-137

megahit

MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Versions: 1.1.4

Arches: generic

Modules: megahit/1.1.4

meme

The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.

Versions: 5.3.0

Arches: generic

Modules: meme/5.3.0

metaeuk

MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.

Versions: 6-a5d39d9

Arches: generic

Modules: metaeuk/6-a5d39d9

minced

MinCED is a program to find Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp.

Versions: 0.3.2

Arches: generic

Modules: minced/0.3.2

miniasm

Miniasm is a very fast OLC-based de novo assembler for noisy long reads.

Versions: 2018-3-30

Arches: generic

Modules: miniasm/2018-3-30

minimap2

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. Mappy provides a convenient interface to minimap2.

Versions: 2.14

Arches: generic

Modules: minimap2/2.14

mirdeep2

miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.

Versions: 0.0.8

Arches: generic

Modules: mirdeep2/0.0.8

mmseqs2

MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets

Versions: 14-7e284

Arches: generic

Modules: mmseqs2/14-7e284

mothur

This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

Versions: 1.48.0

Arches: generic

Modules: mothur/1.48.0

motioncor2

MotionCor2 is a multi-GPU program that corrects beam-induced sample motion recorded on dose fractionated movie stacks. It implements a robust iterative alignment algorithm that delivers precise measurement and correction of both global and non-uniform local motions at single pixel level, suitable for both single-particle and tomographic images. MotionCor2 is sufficiently fast to keep up with automated data collection.

Versions: 1.5.0

Arches: generic

Modules: motioncor2/1.5.0

mummer

MUMmer is a system for rapidly aligning entire genomes.

Versions: 3.23

Arches: generic

Modules: mummer/3.23

mummer4

MUMmer is a versatil alignment tool for DNA and protein sequences.

Versions: 4.0.0rc1

Arches: generic

Modules: mummer4/4.0.0rc1

muscle

MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW.

Versions: 3.8.1551

Arches: generic

Modules: muscle/3.8.1551

ncbi-rmblastn

RMBlast search engine for NCBI

Versions: 2.11.0

Arches: generic

Modules: ncbi-rmblastn/2.11.0

ncbi-toolkit

NCBI C++ Toolkit

Versions: 26_0_1

Arches: generic

Modules: ncbi-toolkit/26_0_1

ncbi-vdb

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. This package contains the interface to the VDB.

Versions: 3.0.0

Arches: generic

Modules: ncbi-vdb/3.0.0

nextflow

Data-driven computational pipelines.

Versions: 22.10.1

Arches: generic

Modules: nextflow/22.10.1

openjdk

The free and opensource java implementation

Versions: 16.0.2, 11.0.17_8

Arches: generic

Modules: openjdk/11.0.17_8, openjdk/16.0.2

openldap

OpenLDAP Software is an open source implementation of the Lightweight Directory Access Protocol. The suite includes: slapd - stand-alone LDAP daemon (server) libraries implementing the LDAP protocol, and utilities, tools, and sample clients.

Versions: 2.4.49

Arches: generic

Modules: openldap/2.4.49

openmpi

An open source Message Passing Interface implementation. The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.

Versions: 4.1.4

Arches: generic

Modules: openmpi/4.1.4

orthofinder

OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.

Versions: 2.5.4

Arches: generic

Modules: orthofinder/2.5.4

orthomcl

OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences.

Versions: 2.0.9

Arches: generic

Modules: orthomcl/2.0.9

parallel

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.

Versions: 20220522

Arches: generic

Modules: parallel/20220522

patchelf

PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.

Versions: 0.16.1

Arches: generic

Modules: patchelf/0.16.1

phylip

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).

Versions: 3.697

Arches: generic

Modules: phylip/3.697

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.

Versions: 2.26.2

Arches: generic

Modules: picard/2.26.2

pilon

Pilon is an automated genome assembly improvement and variant detection tool.

Versions: 1.22

Arches: generic

Modules: pilon/1.22

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

Versions: 1.07

Arches: generic

Modules: plink/1.07

pmix

The Process Management Interface (PMI) has been used for quite some time as a means of exchanging wireup information needed for interprocess communication. However, meeting the significant orchestration challenges presented by exascale systems requires that the process-to-system interface evolve to permit a tighter integration between the different components of the parallel application and existing and future SMS solutions. PMI Exascale (PMIx) addresses these needs by providing an extended version of the PMI definitions specifically designed to support exascale and beyond environments by: (a) adding flexibility to the functionality expressed in the existing APIs, (b) augmenting the interfaces with new APIs that provide extended capabilities, (c) forging a collaboration between subsystem providers including resource manager, fabric, file system, and programming library developers, (d) establishing a standards-like body for maintaining the definitions, and (e) providing a reference implementation of the PMIx standard that demonstrates the desired level of scalability while maintaining strict separation between it and the standard itself.

Versions: 4.1.2

Arches: generic

Modules: pmix/4.1.2

prokka

Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.

Versions: 1.14.6

Arches: generic

Modules: prokka/1.14.6

r

R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

Versions: 4.2.0

Arches: generic

Modules: r/4.2.0

raxml-ng

RAxML-NG is a phylogenetic tree inference tool which uses maximum- likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. RAxML-NG is a successor of RAxML (Stamatakis 2014) and leverages the highly optimized likelihood computation implemented in libpll (Flouri et al. 2014).

Versions: 1.0.2

Arches: generic

Modules: raxml-ng/1.0.2

ray

Parallel genome assemblies for parallel DNA sequencing

Versions: 2.3.1

Arches: generic

Modules: ray/2.3.1

rclone

Rclone is a command line program to sync files and directories to and from various cloud storage providers

Versions: 1.59.1

Arches: generic

Modules: rclone/1.59.1

recon

RECON: a package for automated de novo identification of repeat families from genomic sequences.

Versions: 1.05

Arches: generic

Modules: recon/1.05

relion

RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).

Versions: 4.0.0, 4.0.1, 3.1.3

Variants: gpu, cpu

Arches: amd, intel, intel+gpu_delay

Modules: relion/cpu/3.1.3+amd, relion/gpu/3.1.3+amd, relion/gpu/3.1.3+intel, relion/cpu/4.0.0+amd, relion/gpu/4.0.0+amd, relion/gpu/4.0.0+intel, relion/3.1.3, relion/4.0.0, relion/cpu/4.0.1+amd, relion/gpu/4.0.1+amd, relion/4.0.1, relion/gpu/4.0.1+intel+gpu_delay, relion/gpu/4.0.1+intel

relion-bbr

A modified version of Relion supporting block-based-reconstruction as described in 10.1038/s41467-018-04051-9.

Versions: 3.1.2

Variants: gpu

Arches: intel

Modules: relion-bbr/gpu/3.1.2+intel

relion-helper

Utilities for Relion Cryo-EM data processing on clusters.

Versions: 0.1, 0.2, 0.3

Arches: generic

Modules: relion-helper/0.1, relion-helper/0.2, relion-helper/0.3

repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

Versions: 4.0.9

Arches: generic

Modules: repeatmasker/4.0.9

repeatmodeler

RepeatModeler is a de-novo repeat family identification and modeling package.

Versions: 1.0.11

Arches: generic

Modules: repeatmodeler/1.0.11

repeatscout

RepeatScout - De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A.

Versions: 1.0.5

Arches: generic

Modules: repeatscout/1.0.5

rnaquast

Quality assessment of de novo transcriptome assemblies from RNA-Seq data rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.

Versions: 2.2.0

Arches: generic

Modules: rnaquast/2.2.0

rsem

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

Versions: 1.3.1

Arches: generic

Modules: rsem/1.3.1

rstudio-server

RStudio is an integrated development environment (IDE) for R.

Versions: 2022.12.0-353

Arches: generic

Modules: rstudio-server/2022.12.0-353

sabre

Sabre is a tool that will demultiplex barcoded reads into separate files. It will work on both single-end and paired-end data in fastq format. It simply compares the provided barcodes with each read and separates the read into its appropriate barcode file, after stripping the barcode from the read (and also stripping the quality values of the barcode bases). If a read does not have a recognized barcode, then it is put into the unknown file.

Versions: 2013-09-27

Arches: generic

Modules: sabre/2013-09-27

satsuma2

Satsuma2 is an optimsed version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).

Versions: 2021-03-04

Arches: generic

Modules: satsuma2/2021-03-04

scallop

Scallop is a reference-based transcriptome assembler for RNA-seq

Versions: 0.10.5

Arches: generic

Modules: scallop/0.10.5

seqprep

SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read.

Versions: 1.3.2

Arches: generic

Modules: seqprep/1.3.2

seqtk

Toolkit for processing sequences in FASTA/Q formats.

Versions: 1.3

Arches: generic

Modules: seqtk/1.3

sickle

Sickle is a tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.

Versions: 1.33

Arches: generic

Modules: sickle/1.33

slurm

Slurm is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters. Slurm requires no kernel modifications for its operation and is relatively self-contained. As a cluster workload manager, Slurm has three key functions. First, it allocates exclusive and/or non-exclusive access to resources (compute nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work (normally a parallel job) on the set of allocated nodes. Finally, it arbitrates contention for resources by managing a queue of pending work.

Versions: 22-05-6-1

Arches: generic

Modules: slurm/22-05-6-1

smartdenovo

SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data.

Versions: master

Arches: generic

Modules: smartdenovo/master

sortmerna

SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data

Versions: 2017-07-13

Arches: generic

Modules: sortmerna/2017-07-13

trimmomatic

A flexible read trimming tool for Illumina NGS data.

Versions: 0.39

Arches: generic

Modules: trimmomatic/0.39

ucx

a communication library implementing high-performance messaging for MPI/PGAS frameworks

Versions: 1.13.1

Arches: generic

Modules: ucx/1.13.1