Merge pull request #245 from gp201/expanded_pathogens_docs

Add documentation for Running Freyja on other pathogens

docs/index.rst

@@ -37,4 +37,5 @@ To ensure reproducibility of results, we provide old (timestamped) barcodes and
    src/wiki/lineage_barcode_extract
    src/wiki/read_analysis_tutorial
    src/wiki/terra_workflow
+   src/wiki/expanded_pathogens
 

docs/src/wiki/command_line_workflow.rst

@@ -1,3 +1,4 @@
+.. _command-line-workflow:
 Command Line Workflow
 -------------------------------------------------------------------------------
 

docs/src/wiki/expanded_pathogens.rst

@@ -0,0 +1,80 @@
+Running Freyja on other pathogens
+-------------------------------------------------------------------------------
+
+This guide provides instructions for analyzing non-SARS-CoV-2 pathogens such as
+influenza or MPox using Freyja. The process is similar to SARS-CoV-2 analysis,
+but with some key differences.
+
+Data Availability
+^^^^^^^^^^^^^^^^^
+
+Data for various pathogens can be found in the following repository:
+`Freyja Barcodes <https://github.com/gp201/Freyja-barcodes>`_
+
+Folders are organized by pathogen, with each subfolder named after the date the
+barcode was generated, using the format ``YYYY-MM-DD``. Barcode files are named
+``barcode.csv``, and reference genome files are named ``reference.fasta``.
+
+.. note::
+        Influenza barcodes are available upon request.
+
+Required Files
+^^^^^^^^^^^^^^
+
+To perform these analyses, you will need the following files for the MPox pathogen:
+
+*       `test.sorted.bam <https://github.com/andersen-lab/Freyja/blob/main/docs/data/test.sorted.bam>`_: Aligned, trimmed, and sorted BAM file
+*       `reference.fasta <https://github.com/gp201/Freyja-barcodes/blob/main/MPX/2024-07-24/reference.fasta>`_: Reference genome file
+*       `barcode.csv <https://github.com/gp201/Freyja-barcodes/blob/main/MPX/2024-07-24/barcode.csv>`_: Barcode file
+
+
+Setting Up Output Directories
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Since you will likely be working with multiple wastewater samples, it is
+advisable to create directories for storing output files:
+
+.. code-block:: sh
+
+        mkdir variants_files depth_files demix_files
+
+
+Analysis Steps
+^^^^^^^^^^^^^^
+
+The first step is to generate a variant file. Use the following command to
+perform this step:
+
+.. code-block:: sh
+
+        freyja variants test.sorted.bam --ref reference.fasta --variants variants_files/test.tsv --depths depth_files/test.depth
+
+Please note that you will be passing the reference genome file provided in the
+pathogen folder as the ``--ref`` argument. In cases where multiple reference
+genomes are present in the reference fasta, you can specify the name of the
+desired reference genome with ``--refname [name-of-reference]``.
+
+Once the variant file is generated, proceed to the de-mixing step with the
+following command:
+
+.. code-block:: sh
+
+        freyja demix variants_files/test.tsv depth_files/test.depth --barcodes barcode.csv --output demix_files/test.output
+
+Please note that you will be passing the barcode file provided in the pathogen
+folder as the ``--barcodes`` argument.
+
+Once you’ve run demix on a bunch of samples, you can aggregate all of
+the output files using the command
+
+.. code-block:: sh
+
+        freyja aggregate demix_files/ --output bunch_of_files.tsv
+
+From there, it’s easy to view the output files in any standard TSV viewer
+(Excel, Numbers, LibreOffice Calc, etc.). You should see something like this:
+
+.. code-block::
+
+                summarized      lineages        abundances      resid   coverage
+        test.tsv        [('Other', 0.999999999530878)]  MPX-A.3 MPX-A.2.2       0.79798000 0.20202000   7.5952064496123075      99.94117915510955