https://github.com/blahah/graphsample

Subsample FASTQ by sampling connected components of a de-Bruijn graph
https://github.com/blahah/graphsample

Last synced: 6 days ago
JSON representation

Subsample FASTQ by sampling connected components of a de-Bruijn graph

• Host: GitHub
• URL: https://github.com/blahah/graphsample
• Owner: blahah
• Created: 2015-05-26T15:49:00.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2015-06-20T00:27:50.000Z (over 9 years ago)
• Last Synced: 2024-04-16T01:01:02.887Z (7 months ago)
• Language: C++
• Size: 383 KB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# graphsample

Subsample FASTQ by sampling connected components of a de-Bruijn graph

Taking a subsample from a FASTQ can lead to poor coverage of some regions in the subsample, causing the subsample to have informational properties that are not representative of the full read set.

`graphsample` addresses this problem by building a [de-Bruijn graph](http://en.wikipedia.org/wiki/De_Bruijn_graph) from the reads, identifying all the [connected components](http://en.wikipedia.org/wiki/Connected_component_%28graph_theory%29), and randomly sampling those components. It outputs the reads that belong to the sampled components.

What's the point? Glad you asked! `graphsample` allows you to take a small subsample from a large set of reads, and use the subsample to optimise the parameters of any tools and algorithms you want to run on the full set.

## Compiling

```bash

$ git clone --recursive https://github.com/Blahah/graphsample.git

$ cd graphsample

$ make

```

## Running

```bash

$ bin/graphsample --help

```