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: 11.7.1, 11.8.0
Arches: generic
Modules: cuda/11.8.0, cuda/11.7.1
cufflinks¶
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: 4.2.6.1, 3.8.1
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: 4.9.4, 7.5.0, 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¶
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: 3.1.3, 4.0.0, 4.0.1
Variants: gpu, cpu
Arches: intel+gpu_delay, intel, amd
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