Bioinformatics software

General Bioinformatics Tools

TODO convert to markdown

The following categories of bioinformatics tools are available through conda:

• Read aligners (e.g., bwa, bowtie2)
• Variant callers (e.g., freebayes, gatk, bcftools)
• File format tools (e.g., samtools, vcftools)
• GWAS tools (e.g., plink, gemma)
• Visualization (e.g., igv, multiqc)
• RNA-seq / transcriptomics (e.g., kallisto, salmon)
• Assemblers (e.g., spades, megahit)

Finding Bioinformatics Tools ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

There are several ways to find bioinformatics tools in conda:

1. Search online (recommended for discovery)

   • Use the Anaconda package search or browse specific channels:
   • Bioconda: https://anaconda.org/bioconda
   • Conda-Forge: https://anaconda.org/conda-forge
   • You can search for tools like:
   • plink
   • bcftools
   • samtools

2. Command-line search From your terminal:

   .. code-block:: bash

    # Search all channels (if configured)
    conda search <package-name>
   
    # Example:
    conda search plink
   
    # If using Mamba (faster alternative to conda)
    mamba search plink
   

   To restrict search to a specific channel:

   .. code-block:: bash

    conda search -c bioconda plink
   

3. Get full list (advanced) You can list everything in a channel, but it's very large:

   .. code-block:: bash

    # List all bioconda packages
    conda search --channel bioconda "*" | less
   

   Tip: pipe it through grep to find specific tools:

   .. code-block:: bash

    conda search -c bioconda "*" | grep vcftools