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Project 6: Linked-Reads QC: Summarize sequencing library quality of 10x Genomics Chromium linked read #6

abaghela opened this Issue Aug 2, 2017 · 3 comments


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abaghela commented Aug 2, 2017

Linked-Reads QC: Summarize sequencing library quality of 10x Genomics Chromium linked reads

The goal of this project is to develop a software tool to quickly report on the quality of a 10x Genomics Chromium linked reads library. The report will summarize the sizes of the molecules, the number of reads per molecule, the number of molecules per barcode, and the amount of DNA per barcode. Inspiration can be taken from FastQC, and the Summary page of the Loupe software of 10x Genomics.


The tool will have two modes of operation: fast and complete. The fast mode will produce a report as quickly as possible by subsampling the data in an intelligent fashion. The complete mode will analyze all of the data and produce a comprehensive report. The analysis will use reads aligned to the reference genome using BWA-MEM, Lariat, or Longranger. A stretch goal is to generate this report de novo without using a reference genome by assembling a small region of the genome and using that assembly as the reference. The report will be compatible with the report aggregating tool MultiQC.

Useful skills

The analysis and report will be created using R, the Tidyverse, RMarkdown, and Flexdashboard. Familiarity with some of these tools is useful, but not necessary to participate in this project. Non-technical participants are welcome to design the aesthetics of the report, prepare and deliver the presentation, and coordinate writing a brief paper about the tool.

Team Lead

Shaun Jackman | | @sjackman | Grad Student | BC Cancer Agency Genome Sciences Centre


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sjackman commented Sep 12, 2017

Required software

  • Bedtools
  • BWA
  • FastQC
  • Graphviz
  • Long Ranger
  • Miller
  • R & RStudio
  • samtools
  • seqtk

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jakelever commented Oct 10, 2017

Hey team lead, we've been gathering Github IDs for your team members. As you've likely been notified, we've created a project repo for you that you are now the admin of and have added the team members to this. We've received almost everyone's Github ID and will continue to add members as we got their Github IDs.

Project repo:

Feel free to rename the repo as appropriate. Note that the repo currently has an MIT license. Amend this as required. It'd be a great idea to start a discussion on this repo with information to get your team members started (e.g. some small suggested reading, things to look up, etc). We will also be adding everyone to Slack and creating a specific channel for each project. This may be an easier way to communicate.

Thanks, Jake
obo the Hackseq organising committee


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sjackman commented Oct 11, 2017

Thanks, Jake!

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