Vendor Software

Software from Scientific Instrument Vendors

Vendor supplied software available as modules.

Oxford Nanopore

  • Nanopolish - Software package for signal-level analysis of Oxford Nanopore sequencing data.
  • fast5 - A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
  • ont-guppy-cpu Guppy is a production basecaller provided by Oxford Nanopore
  • Python libraries
    • NanoComp - Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.
    • NanoFilt - Filtering and trimming of Oxford Nanopore Sequencing data
    • nanoget - Functions to extract information from Oxford Nanopore sequencing data and alignments.
    • nanomath - Provides a few simple math and statistics functions for other scripts processing Oxford Nanopore sequencing data
    • NanoPlot - Plotting suite for Oxford Nanopore sequencing data and alignments
    • nanoplotter - Plotting functions of Oxford Nanopore sequencing data
    • NanoStat - Calculate statistics for Oxford Nanopore sequencing data and alignments
    • pauvre - Tools for plotting Oxford Nanopore and other long-read data.
    • Porechop - Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.


  • bam2fastx - Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded dat.


  • blc2fastq
  • illumina-dump (SRA-Toolkit)
  • BaseSpace Command line tools
  • Strelka 2

10X Genomics

Refernce data for 10X Genomics tools is located /shared/biodata/ngs/Reference/10X

  • Cell Ranger
  • Cellranger ATAC
  • Cell Ranger ARC
  • Space Ranger


Gurobi Optimizer is commerical software. Gurobi is a solver for LP, QP and MIP problems. Gurobi provides individual academic licenses. If you want to use Gurobi, apply for your personal license. Once your license is granted, you can activate the software license. Load the latest Gurobi module and run grbgetkey using the argument provided on the Academic License. (example: grbgetkey ae36ac20-16e6-acd2-f242-4da6e765fa0a) The grbgetkey will write a personal license file into your UNIX home directory.

Open Source Tools

Open source tools for reading sequence data from

  • SRA Toolkit - The Sequence Read Archive (SRA Toolkit) stores raw sequence data from “next-generation” sequencing technologies
  • Strelka - Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
  • Unicycler - Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.