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Available bioinformatics resources/tools on Tufts HPC

Mailing List (E-list)

To stay updated on bioinformatics education, software tools, and workshop notifications, subscribe to our e-list: best@elist.tufts.edu.

In the future, we will post workshop notifications and resources through this email list.

Workshops and resources

Tufts Research Technology Guides website (In development)

Coming in November 2024. Stay tuned for updates! hpcdocu

Current Workshops, stop updating once our new website is online.

Bioinformatics workshops provided by TTS Research Technology in 2022, 2023, 2024](https://tuftsdatalab.github.io/tuftsWorkshops/)

Archived Workshops

Archived TTS Datalab bioinformatics workshops

Other Workshops

Bioinformatics workshops provided by Bioinformatics Education and Services at Tufts

Website

Bioinformatics website (Last updated July 2023)

Note: Some materials may be outdated, so always verify the relevance of content before applying it to your projects.

Tools on the Cluster

Use module avail to check the full list of tools available on the cluster. Below are some commonly used tools:

   abcreg/0.1.0                         kallisto/0.48.0                     (D)    orthofinder/2.5.5          
   abyss/2.3.7                          kneaddata/0.12.0                           pandaseq/2.11
   alphafold/2.3.0                      kraken2/2.1.3                              parabricks/4.0.0-1
   alphafold/2.3.1                      krakentools/1.2                            parabricks/4.2.1-1         
   alphafold/2.3.2                      macs2/2.2.7.1                        
   amplify/2.0.0                        macs3/3.0.0a6                              pepper_deepvariant/r0.8    
   angsd/0.939                          masurca/4.0.9                              petitefinder/cpu
   angsd/0.940                   (D)    masurca/4.1.0                       (D)    picard/2.25.1
   bakta/1.9.3                          medaka/1.11.1                              picard/2.26.10              
   bbmap/38.93                          megahit/1.2.9                              plink/1.90b6.21            
   bbmap/38.96                   (D)    meme/5.5.5                                 plink2/2.00a2.3
   bbtools/39.00                        metaphlan/4.0.2                            polypolish/0.5.0
   bcftools/1.13                        metaphlan/4.0.6                     (D)    preseq/3.2.0
   bcftools/1.14                        miniasm/0.3_r179                           prokka/1.14.6
   bcftools/1.17                        minimap2/2.26                       (D)    qiime2/2023.2
   bcftools/1.20                 (D)    minipolish/0.1.3                           qiime2/2023.5
   beast2/2.6.3                         mirdeep2/2.0.1.3                           qiime2/2023.7
   beast2/2.6.4                         mirge3/0.1.4                               qiime2/2023.9
   beast2/2.6.6                  (D)    mothur/1.46.0                              qiime2/2024.2             
   ... ...

A few tips

  1. Before installing your own tools, check if they are already available on the cluster using the module avail command.

  2. Always be aware of the software versions, especially when using scripts from colleagues.

  3. For less common tools, consider installing them yourself to ensure you have full control over the version and availability.

We will cover how to install tools from source code in our upcoming workshop. If you need to install a tool not commonly used, it's best to do it yourself to avoid issues with maintenance. Stay tuned for a detailed guide!

Open OnDemand APPs

You can access Open OnDemand through this link

Bioinformatics Apps

We offer a wide range of bioinformatics tools as apps, including AlphaFold and CellProfiler. Additionally, 31 nf-core pipelines are available as apps for ease of use, with the most popular being nf-core/rnaseq, which we will demonstrate in our final workshop.

bio app

RStudio and Shinyngs Apps

RStudio Pax, use R/4.4.1 which has the most comprehensive packages installed (1300+). rstudio

RStudio Pax screenshot

We will demenstrate how to install packages in our next workshop

RStudio is available on Open OnDemand, with different versions tailored for specific tasks. For example, in RStudio for scRNA-Seq, the most commonly used packages for scRNA-Seq analysis are pre-installed to help streamline your workflow.

Other Apps

We also provide other applications like Jupyter Bioinfo, JupyterLab, Jupyter Notebook, IGV, and Galaxy to support your daily research activities.

nf-core pipelines

Use module avail nf-core to get the list of nf-core pipelines deployed on cluster

modules

   nf-core-ampliseq/2.8.0                     nf-core-nanostring/1.3.0      (D)
   nf-core-ampliseq/2.9.0                     nf-core-pairgenomealign/1.0.0
   nf-core-ampliseq/2.10.0                    nf-core-pangenome/1.1.0
   nf-core-ampliseq/2.11.0             (D)    nf-core-pangenome/1.1.1
   nf-core-atacseq/2.1.2                      nf-core-pangenome/1.1.2       (D)
   nf-core-bacass/2.2.0                       nf-core-proteinfold/1.1.0
   nf-core-bacass/2.3.1                (D)    nf-core-raredisease/2.0.1
   nf-core-bamtofastq/2.1.1                   nf-core-rnafusion/3.0.1
   nf-core-chipseq/2.0.0                      nf-core-rnafusion/3.0.2       (D)
   nf-core-denovotranscript/1.0.0             nf-core-rnaseq/3.14.0
   nf-core-detaxizer/1.0.0                    nf-core-rnasplice/1.0.2
   nf-core-differentialabundance/1.4.0        nf-core-rnasplice/1.0.3
   nf-core-differentialabundance/1.5.0 (D)    nf-core-rnasplice/1.0.4       (D)
   nf-core-eager/2.5.1                        nf-core-sarek/3.4.0
   nf-core-fetchngs/1.11.0                    nf-core-sarek/3.4.1
   nf-core-fetchngs/1.12.0             (D)    nf-core-sarek/3.4.3
   nf-core-funcscan/1.1.4                     nf-core-sarek/3.4.4           (D)
   nf-core-funcscan/1.1.5              (D)    nf-core-scrnaseq/2.5.1
   nf-core-hic/2.1.0                          nf-core-scrnaseq/2.7.0
   nf-core-mag/2.5.2                          nf-core-scrnaseq/2.7.1        (D)
   nf-core-mag/2.5.4                          nf-core-smrnaseq/2.3.0
   nf-core-mag/3.0.0                          nf-core-smrnaseq/2.3.1        (D)
   nf-core-mag/3.0.2                   (D)    nf-core-taxprofiler/1.1.5
   nf-core-metatdenovo/1.0.0                  nf-core-taxprofiler/1.1.6
   nf-core-metatdenovo/1.0.1           (D)    nf-core-taxprofiler/1.1.7
   nf-core-methylseq/2.6.0                    nf-core-taxprofiler/1.1.8     (D)
   nf-core-nanoseq/3.1.0                      nf-core-viralrecon/2.6.0
   nf-core-nanostring/1.2.1

Open OnDemand apps

nfcoreapp

Contact Us

We are part of the TTS Research Technology team. Our services are not limited to bioinformatics; we also support data science, statistics, and research data management.

For consultations, please submit a ticket to tts-research@tufts.edu.

For more details, visit our page: Research Technology Consulting Services.