Common software available on the Tufts high-performance computing research cluster

Some commonly uses software titles available on the research cluster are:

  • Matlab: high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numerical computation
  • STATA: full data-management system with complete statistical and graphical capabilities
  • Bowtie: ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome
  • TopHat: aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions
  • Cufflinks: assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
  • SAMtools: provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
  • BamTools: provides both a programmer’s API and end-user’s toolkit for handling BAM files
  • Mothur: This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community
  • RSEM: a software package for estimating gene and isoform expression levels from RNA-Seq data

See UIT Research Computing Software for further details and a complete list of software.

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