Software
Below is a list of software available on BisonNet. Most software packages are added and removed from your environment using Environment Modules (e.g. module load matlab). If you need additional software, please submit a request by emailing bisonnet@bucknell.edu.
Also, some software packages have specific instructions that are necessary to follow.
| Software | Version | Description | Module |
|---|---|---|---|
| augustus | 3.4.0 | Predicts genes in eukaryotic genomic sequences | assembly_assessment |
| bamtools | 2.5.2 | Manipulate BAM (genetic sequence) files | assembly_assessment |
| BBTools | 2023.02.06 | BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data | assembly_assessment |
| BCFTools | 1.17 | BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF | bcftools |
| Beast2 | 2.7.0 | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. | beast2 |
| bedtools | 2.30.0 | Manipulate bed format files | seq_tools |
| BioPerl | 1.7.8 | Perl tools for bioinformatics, genomics, and life science | seq_tools |
| bowtie2 | 2.5.1 | Map reads to a reference genome | alignment (python/3.10-bio) |
| bracken | 2.7 | Bayesian Reestimation of Abundance with KrakEN | kraken2 |
| Braker2 | 2.1.5 | BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes | braker2 |
| BUSCO | 5.4.5 | Measures quality of assembly | assembly_assessment (python/3.10-bio) |
| BUSCO-phylogenomics | 1/12/2021 | Utility script to construct species phylogenies using BUSCOs | BUSCO-phylogenomics |
| canu | 2.2 | A single molecule sequence assembler for genomes large and small. | assembly |
| COMSOL Multiphysics | 6.0 | A finite element analysis, solver and multiphysics simulation software | comsol |
| CUDA | 11.6.2 | The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications. | CUDA |
| cudnn | 8.4.0 | The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. | cudnn |
| DRAP | 1.92 | De novo RNA-seq Assembly Pipeline | DRAP |
| dvr-scan | 1.5.1 | Find and extract motion events in videos. | python/3.10-misc |
| EMBOSS | 6.6 | Manipulating sequence files, among other things | seq_tools |
| EVidence Modeler | 1.1.1 | The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures | annotation |
| exonerate | 2.2.0 | Exonerate is a generic tool for pairwise sequence comparison | exonerate |
| fastp | 0.23.2 | A tool designed to provide fast all-in-one preprocessing for FastQ files. | qc, fastp |
| faSomeRecords (python) | Retrieve fasta sequences from a multi-fasta file | seq_tools | |
| fasta-splitter.pl | 0.2.6 | Split FASTA files | seq_tools |
| FastQC | 0.11.9 | To assess the quality of DNA sequence data | qc |
| fastx-toolkit | 0.0.14 | To perform basic manipulations on DNA sequence data | qc |
| ffmpeg | 5.1 | AV conversion tools | ffmpeg |
| Funannotate | 2021-01.12 | Funannotate is a genome prediction, annotation, and comparison software package | funannotate |
| Gaussian | 16.B.01 | Computational chemistry | gaussian |
| gcc/g++/gfortran | 8.5.0 | Open source compiler collection | (none required) |
| GCTA | 1.94.1 | Genome-wide Complex Trait Analysis | seq_tools |
| GMAP | 12/17/2021 | GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program | alignment |
| Gurobi Optimizer | 10.0.1 | An optimization solver for linear programming (LP), quadratic programming (QP), quadratically constrained programming (QCP), mixed integer linear programming (MILP), mixed-integer quadratic programming (MIQP), and mixed-integer quadratically constrained programming (MIQCP) | gurobi-optimizer |
| HISAT2 | 2.2.1 | graph-based alignment of next generation sequencing reads to a population of genomes | alignment |
| hmmer | 3.3.2 | Used for searching sequence databases for sequence homologs and for making sequence alignments | assembly_assessment |
| HTStream | 1.3.0 | Quality control pipeline for High Throughput Sequencing data | qc |
| IBAMR | 0.7.10.11.0 | An adaptive and distributed-memory parallel implementation of the immersed boundary (IB) method | (not a module) |
| ILOG CPLEX Studio | 22.1.1 | A mathematical optimization software package | CPLEX |
| ipyrad | 0.9.90 | Assembly and analysis of RAD-seq type genomic data sets | radseq (python/3.10-bio) |
| IQtree | 1.6.12 | Build phylogenetic trees from sequences | phylogeny |
| I-TASSER | 5.2 | Iterative Threading ASSEmbly Refinement | I-TASSER |
| JAGS | 4.3.2 | JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. | JAGS |
| java | Java SE Development Kit | java |
|
| jellyfish | 2.3.0 | Tool for fast, memory-efficient counting of k-mers in DNA | alignment |
| jmodeltest2 | 2.1.10 | Find the best model of sequence evolution for building phylogenies | phylogeny |
| kallisto | 0.46.1 | Map reads to a reference genome (without sketchiness) | alignment |
| Kraken2 | 2.1.1 | A taxonomic classification system | kraken2 |
| LAMMPS Molecular Dynamics Simulator | 2022.09.02 | LAMMPS is a classical molecular dynamics code with a focus on materials modeling. | lammps |
| MAFFT | 7.505 | Align sequences | alignment |
| magma | 2.27-4 | Magma is a software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics. | magma |
| Maker | 3..01.03 | MAKER is a portable and easily configurable genome annotation pipeline. | annotation |
| Mathematica | 13 | A modern technical computing system spanning most areas of technical computing — including neural networks, machine learning, image processing, geometry, data science, visualizations, and others. | mathematica |
| MATLAB | R2023a | Multi-paradigm numerical computing environment and programming language | matlab |
| metaeuk | 2023.02.06 | Sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics | assembly_assessment |
| MrBayes | 3.2.7a | Building phylogenies | phylogeny |
| MultiQC | 1.14 | Aggregate results from bioinformatics analyses across many samples into a single report | python/3.10-bio |
| nbo6 | 2023-02-22 | NBO6 for Gaussian | gaussian |
| ncbi-BLAST+ | 2.13.0+ | BLAST alignment to database. $NCBI_DATA set to top-level of weekly database downloads. | ncbi-blast |
| Oases | 0.2.09 | De novo transcriptome assembler for very short reads | assembly |
| Octave | 7.2.0 | Powerful mathematics-oriented syntax with built-in 2D/3D plotting and visualization tools | octave |
| OpenCV | 4.6.0 | Open source Computer Vision | opencv |
| openmpi | 4.1.4 | Message Passing Interface project, generally used for running parallel code. | openmpi |
| PAL2NAL | 14 | Force nucleotides onto protein alignments | alignment |
| PAML | 4.9j | Testing genes for selection | molecular_evolution |
| PARI/GP | 2.13.4 | PARI/GP is a widely used computer algebra system designed for fast computations in number theory | pari |
| PASA | 2.5.2 | PASA Pipeline | PASA |
| Perl | 5.36.0 | General purpose programming language | perl |
| plink | 1.90 | PLINK is a free, open-source whole genome association analysis toolset | plink |
| prodigal | 2.6.3 | Prodigal Gene Prediction Software | assembly_assessment |
| pysam | 0.21.0 | Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. | python/3.10-bio |
| PySPH | 1.0b1 | A framework for Smoothed Particle Hydrodynamics in Python | python/3.10-misc |
| Python | 3.10 | General purpose programming language (See modules list) | python |
| R | 4.2.1 | Software environment for statistical computing and graphics | R |
| RELION | 4.0 | relion (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a software package that employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination. | RELION |
| RSEM | 1.3.3 | Calculates read counts from BAM files | alignment |
| Sage | 9.6 | SageMath is a free open-source mathematics software system | sage |
| salmon | 1.9.0 | Map reads to a reference genome (wicked fast) | alignment |
| samtools | 1.16.1 | Manipulate sam and bam files | seq_tools |
| SAS | 9.4 | Statistical software suite for data management, advanced analytics, multivariate analysis, business intelligence, criminal investigation, and predictive analytics. | SAS |
| Scaff10X | 5 | Pipeline for scaffolding and breaking a genome assembly using 10x genomics linked-reads | assembly |
| seqtk | 1.3 | Toolkit for processing sequences in FASTA/Q formats | seq_tools |
| SIMULIA | 2022 | Software suite, including Abaqus and Tosca, for finite element analysis and computer-aided engineering | SIMULIA |
| SOAP de novo | r242 | Assembling genomes | assembly |
| SPAdes | 3.15.4 | It’s all about the viruses: new coronaSPAdes, rnaviralSPAdes and metaviralSPAdes pipelines. | SPAdes |
| SRA_Toolkit | 3.0.0 | Downloads files from the Sequence Read Archive | seq_tools |
| stacks | 2.65 | Population genetics with RAD data | stacks |
| STAR | 2.7.10 | Map reads to a reference genome | alignment |
| stringtie | 2.2.1 | Transcript assembly and quantification for RNA-Seq | assembly |
| Tensorflow | 2.12.0 | Maching learning platform | python/3.10-deeplearn |
| TensorRT | 8.4.3.1 | NVIDIA® TensorRT™, an SDK for high-performance deep learning inference | TensorRT |
| TopHat | 2.1.1 | TopHat is a fast splice junction mapper for RNA-Seq reads. | alignment |
| TransDecoder | 5.5.0 | Identifies candidate coding regions within transcript sequences | transdecoder |
| trimmomatic | 0.39 | To trim bad quality sequence data | qc |
| Trinity (singularity) | 2.13.2 | For transcriptome assembly | Trinity |
| Trinnotate | 4.0.0 | For transcriptome assembly annotation | Trinotate |
| vcftools | 0.1.16 | Manipulate vcf files | seq_tools |
| Velvet | 1.2.10 | Sequence assembler for very short reads | assembly |
| VEP | 107 | Variant Effect Predictor | seq_tools |
| XCrySDen | 1.6.2 | XCrySDen is a crystalline and molecular structure visualisation program | xcrysden |
| xmgrace | 5.1.25 | 2D plotting tool | xmgrace |