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Deduper

Part 1

Use this repo template to create your own Deduper repo - you should do all your work in your own repository. Please name it Deduper-<github-user-name>.

Write up a strategy for writing a Reference Based PCR Duplicate Removal tool. That is, given a sorted sam file of uniquely mapped reads, remove all PCR duplicates (retain only a single copy of each read). Develop a strategy that avoids loading everything into memory. You should not write any code for this portion of the assignment. Be sure to:

  • Define the problem
  • Write examples:
    • Include a properly formated sorted input sam file
    • Include a properly formated expected output sam file
  • Develop your algorithm using pseudocode
  • Determine high level functions
    • Description
    • Function headers
    • Test examples (for individual functions)
    • Return statement

For this portion of the assignment, you should design your algorithm for single-end data, with 96 UMIs. UMI information will be in the QNAME, like so: NS500451:154:HWKTMBGXX:1:11101:15364:1139:GAACAGGT. Discard any UMIs with errors (or think about how you might error correct, if you're feeling ambitious).

Part 2

An important part of writing code is reviewing code - both your own and other's. In this portion of the assignment, you will be assigned 3 students' pseudocode algorithms to review. Be sure to evaluate the following points:

  • Does the proposed algorithm make sense to you? Can you follow the logic?
  • Does the algorithm do everything it's supposed to do? (see part 1)
  • Are proposed functions reasonable? Are they "standalone" pieces of code?

You can find your assigned reviewees on Canvas. You can find your fellow students' repositories at

github.com/<user>/Deduper-<github-user-name>

Be sure to leave comments on their repositories by creating issues or by commenting on the pull request.

Part 3

Write your deduper function!

Given a SAM file of uniquely mapped reads, and a text file containing the known UMIs, remove all PCR duplicates (retain only a single copy of each read). Remember:

  • Your Python code can assume a sorted sam file (you might need to use samtools sort outside of your Python script)
  • Account for:
    • all possible CIGAR strings (including adjusting for soft clipping, etc.)
    • Strand
    • Single-end reads
    • Known UMIs
  • Considerations:
    • Millions of reads – avoid loading everything into memory!
    • Be sure to utilize functions appropriately
    • Appropriately comment code and include doc strings
  • CHALLENGE: In a separate branch, implement options for
    • Single-end vs paired-end
    • Known UMIs vs randomers
    • Error correction of known UMIs
    • Choice of duplicate written to file

You MUST:

  • Write Python 3.11 compatible code
  • Include the following argparse options
    • -f, --file: designates absolute file path to sorted sam file
    • -o, --outfile: designates absolute file path to sorted sam file
    • -u, --umi: designates file containing the list of UMIs
    • -h, --help: prints a USEFUL help message (see argparse docs)
      • That is, your code must be able to run (in a single step) if given a command in the format: 
        ./<your_last_name>_deduper.py -u STL96.txt -f <in.sam> -o <out.sam>
  • Output the first read encountered if duplicates are found
  • Output a properly formatted SAM file
  • Name your python script <your_last_name>_deduper.py and place it in the top level of your repo (that is, not inside a folder)