https://github.com/hanfang/Topsorter

Graphical assessment of structrial variants using 10x genomics data
https://github.com/hanfang/Topsorter

genomics graph topological-sort

Last synced: about 2 months ago
JSON representation

Graphical assessment of structrial variants using 10x genomics data

• Host: GitHub
• URL: https://github.com/hanfang/Topsorter
• Owner: hanfang
• Created: 2016-10-26T20:49:11.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2017-02-23T22:19:03.000Z (over 7 years ago)
• Last Synced: 2023-10-20T20:09:24.111Z (8 months ago)
• Topics: genomics, graph, topological-sort
• Language: Python
• Homepage:
• Size: 67.4 KB
• Stars: 10
• Watchers: 6
• Forks: 2
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Lists

• awesome-linked-reads - Topsorter - commit/hanfang/Topsorter?label=%20) (Tools)

README

        
# Topsorter

### - Graphical assessment of structrial variants using 10x genomics data

####  

![alt text](https://github.com/hanfang/Topsorter/blob/master/image/topsorter.png)

### Contact

- Han Fang ([email protected])

- Srividya Ramakrishnan ([email protected])

- Fritz Sedlazeck ([email protected])

--------

### Topsorter

#### Traversing & finding the longest path (most confident haplotype) in a weighted directed acyclic graph (DAG).

- At the initial construction step, it splits regions of a chromosome by structural variants and creates a weighted DAG.

- Then it updates the weights of the edges according to barcodes information (and/or other quality metrics) from the script barcode_profiles.py.

- Finally Topsorter performs topological sorting of the graph and finds the longest path (the most confident haplotype).

- Input: vcf file

- Output: PDF files of graphs for each chromosme, longest paths

- Command: `python topsorter.py $vcf ` 

-------- 

### BarcodeProfiler

#### Building barcode profile for the alignments and count the overlapping barcodes for every split region of a chromosome 

-  Extract alignments from every split region in to a bam file and index them

-  Identify the barcodes in each of these split regions and count number of reads per barcode

-  Count the barcode overlaps between the  split regions of interest

-  Input: Phased bam file from 10x data, Constructed split regions in bed format using Topsorter class (func exportVCFBed )

-  Output: directory containing files

         overlapping_reads.bam

         overlapping_reads.bam.bai

         reads_barcode_profile.txt

         barcode_overlaps_between_regions.txt

   

-  Command: ./barcode_profiles.py -bam \ -bed \ -o \