Tufts Bioinformatics Resources

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

Current Workshops

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

Note: Some materials may be outdated, so always verify the relevance of content before applying it to your projects.

A new documentation website is coming in November 2024. Stay tuned for updates!

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

Before installing your own tools, check if they are already available on the cluster using the module avail command.
Always be aware of the software versions, especially when using scripts from colleagues.
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!

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.