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Applications, Packages and Environment Images

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  • Registry Location: https://bioconda.github.io/recipes/samtools/README.html

  • “Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools - Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format, BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants, HTSlib - A C library for reading/writing high-throughput sequencing data” - Source: https://www.htslib.org/

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > bsub -G ${group_name} -Is -q general-interactive -a 'docker(quay.io/biocontainers/samtools:1.2-0)' /bin/bash

Seurat

seurat-scripts

  • Registry Location: https://bioconda.github.io/recipes/seurat-scripts/README.html

  • “A set of wrappers for individual components of the Seurat package. …this package adds a set of simple wrappers with robust argument parsing. …ultimate objective is to have language-agnostic intermediate formats allowing composite workflows using a variety of software packages.” - Source: https://bioconda.github.io/recipes/seurat-scripts/README.html

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > bsub -G ${group_name} -Is -q general-interactive -a 'docker(quay.io/biocontainers/seurat-scripts:0.0.6--0)' R

Shiny

  • Registry Location: https://hub.docker.com/r/rocker/shiny

  • “Shiny is an R package that makes it easy to build interactive web apps straight from R.” - Source: https://shiny.rstudio.com/

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > bsub -G ${group_name} -Is -q general-interactive -a 'docker(rocker/shiny)' R

SingleR

SnpSift

STAR

SRA Toolkit

  • Registry Location:

  • “The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format to the following formats: ABI SOLiD native (colorspace fasta / qual), fasta, fastq, sff, sam (human-readable bam, aligned or unaligned), Illumina native…” - Source: https://www.ncbi.nlm.nih.gov/books/NBK158900/

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > PATH="/usr/local/ncbi/sra-tools/bin:$PATH" bsub -G ${group_name} -Is -q general-interactive -a "docker(inutano/sra-toolkit:latest)" /bin/sh

Strelka2

  • Registry Location: https://bioconda.github.io/recipes/strelka/README.html

  • “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.” - Source: https://github.com/Illumina/strelka

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > bsub -G ${group_name} -Is -q general-interactive -a 'docker(quay.io/biocontainers/strelka:2.9.10--0)' /bin/bash

TopHat

  • Registry Location: https://bioconda.github.io/recipes/tophat/README.html

  • “TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.” - Source: http://ccb.jhu.edu/software/tophat/index.shtml

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > bsub -G ${group_name} -Is -q general-interactive -a 'docker(quay.io/biocontainers/tophat:2.1.1--py27_3)' /bin/bash

Valgrind

  • Registry Location: https://hub.docker.com/r/greymail/gcc-cmake-valgrind

  • “Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.” - Source: https://valgrind.org/

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > bsub -G ${group_name} -Is -q general-interactive -a 'docker(greymail/gcc-cmake-valgrind:0.1)' /bin/bash

Varscan

  • Registry Location: https://bioconda.github.io/recipes/varscan/README.html

  • “VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation.” - Source: http://dkoboldt.github.io/varscan/

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > bsub -G ${group_name} -Is -q general-interactive -a 'docker(quay.io/biocontainers/varscan:2.3.7--3)' /bin/bash

VCFtools

Velocyto

  • Registry Location: https://hub.docker.com/r/genomicpariscentre/velocyto

  • “Velocyto is a package for the analysis of expression dynamics in single cell RNA seq data.” - Source: http://velocyto.org/

  • Run interactive job:
    Code Block
    languagepython
    linenumbersfalse
    > PATH="/opt/conda/bin:$PATH" bsub -G ${group_name} -Is -q general-interactive -a "docker(genomicpariscentre/velocyto)" /bin/bash
  • Activate conda environment:
    Code Block
    languagepython
    linenumbersfalse
    > conda activate base

    • You will now be able to use velocyto command.

  • If you encounter an error stating your shell has not been properly configured, please see this section on initializing your shell to use conda.

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