2.

Bioinformatics services

a.

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Access to Emboss software is available on emboss.uit.tufts.edu , which provides both shell and web access. In both cases you will need an account. You may request an account at  http://research.uit.tufts.edu . The server hardware is a single quad core 64 bit host with 4 gig of ram.

For shell access to command line tools:
> ssh -Y emboss.uit.tufts.edu

For access to the web interface wEmboss.

For access to emboss web documentation.

Emboss tutorial

If you have any questions about Emboss related usage, applications, or assistance with software, please contact bio-support@tufts.edu.

b. Tufts Center for Neuroscience Research Genomics Core

The Tufts CNR Genomics Core supplies links to bioinformatics resources related to their operation. See Tufts CNR Genomics Core Resources for more information.

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Timings for Genome Mapping

The newest update to SLURM has better handling of backfill, which means if you specify a expected time for your program to run it can be placed earlier as nodes open up. Using sbatch you can specify a limit on the total run-time with -t or --time d-h:m:s. Times can be specified as min, min:sec, hr:min:sec, day-hr, day-hr:min, and day-hr:min:sec. So -t 5 means five minutes -t 5:00:00 is five hours.

Here are some approximate run times (min sec) for BWA-mem, bowtie2, and samtools with 7, 15, 30, and 60 million fastq sequences. Samtools was used to convert SAM files and then sort the resulting BAM files.  These runs were done with 8 cores and 16 GB memory. The timings were obtained using the time command  ( e.g. time bwa mem -t 8  <hg38 ref> <sequences (human)> ) though some  programs report the runtimes in the output. To effectively use the back fill, take note of how long your programs run and add a bit more time to give your programs some extra run time using the -t or --time parameter.  Make sure to add run times for workflows, e.g. a bwa mem  run followed by  samtools reformatting as well as accounting for multiple runs, e.g. processing 6 fastq files. 

b. Genome Indexes on Cluster

Several mammalian and model system genomes, indexes, and annotations are located on the Tufts HPC cluster.  Currently the genomes are listed below in the indicated directory tree are UCSC genome builds, except for canFam3 which is a NCBI build.

/cluster/tufts/genomes
  /HomoSapiens
    /hg18
    /hg19
    /hg38 (New)
  /MusMusculus
    /mm9
    /mm10
  /RattusNorvegicus
    /rn4
    /rn5
    /rn6 (New)

  /CanisFamiliaris
    /canFam2
    /canFam3

  /BosTaurus
    /bosTau7
  /EquusCaballus
    /equCab2
  /GallusGallus
    /galGal4
  /SusScrofa
    /susScr3

  /DrosophilaMelanogaster
    /dm3
    /dm6 (New)
  /CaenorhabditisElegans
    /ce10 
  /DanioRerio
    /danRer7
    /danRer10 (New)
 /SaccharomycesCerevisiae  (no Transcriptome)
    /sacCer2   
    /sacCer3 

  /Annotation
  /Sequence

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  module load bowtie2

  export BOWTIE2_INDEXES=/cluster/tufts/genomes/MusMusculus/mm10/Sequence/Bowtie2Index
  export MYDATADIR=/cluster/shared/myutln/mmdata
  
  bowtie2 -q -x genome -1 $MYDATADIR/myreads_1.fq -2 $MYDATADIR/myreads_2.fq -S $MYDATADIR/myreads.sam

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c. HPC Modules for Bioinformatics

  Note: some bioinformatic software modules, such as R modules like bioconductor or python modules, are not listed here because they are part of a larger module, for example R/3.1.0 or python/2.7.6. Load those modules to get to bioconductor or python modules such as numpy or matplotlib.

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Application performance is not always well documented and it may be beneficial to you to do some benchmarking.  By doing so you will be in a position to better utilize the cluster resources. For example here is a benchmark examination of blastp and other tools.  

d. Tufts Center for Neuroscience Research Genomics Core

The Tufts CNR Genomics Core supplies links to bioinformatics resources related to their operation. See Tufts CNR Genomics Core Resources for more information.

Misc

A separate server is used to support these services in some cases. However some software may require installation on the linux research cluster. Check the Installed Software for Bioinformatic software available on the cluster. To make a special request for software installation, please follow the instructions as noted elsewhere on this page.