https://github.com/gedankenstuecke/genomeskimming

scripts for the genome skimming paper
https://github.com/gedankenstuecke/genomeskimming

Last synced: 8 days ago
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scripts for the genome skimming paper

• Host: GitHub
• URL: https://github.com/gedankenstuecke/genomeskimming
• Owner: gedankenstuecke
• Created: 2015-04-10T06:55:33.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2015-05-20T06:57:28.000Z (over 9 years ago)
• Last Synced: 2024-11-13T14:25:37.164Z (2 months ago)
• Language: Shell
• Homepage:
• Size: 27.3 MB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Genome Skimming

This repository contains the scripts used for generating and analysing the data for the paper *Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens*. 

## Requirements

I used [*MIRA*](mira-assembler.sourceforge.net), [*Omega*](http://omega.omicsbio.org/), [*sga*](https://github.com/jts/sga), [*SPAdes*](http://bioinf.spbau.ru/spades), [*Velvet/Optimiser*](https://github.com/tseemann/VelvetOptimiser) and [*MetaVelvet*](metavelvet.dna.bio.keio.ac.jp), which you should have installed if you want to recreate the whole analysis. Besides that's the various scripts for generating the data and analysing the assemblies will have their own dependencies: 

- Python 2.x

 - [BioPython](http://biopython.org/wiki/Main_Page)

 - [Pysam](http://biopython.org/wiki/Main_Page)

- [ART](http://www.niehs.nih.gov/research/resources/software/biostatistics/art/)

- [FLASH](ccb.jhu.edu/software/FLASH/)

- [bbmap](bbmap.sourceforge.net)

- [QUAST](http://quast.bioinf.spbau.ru/)

## Structure

### 00-simulate_reads

This folder contains the files needed to generate twin data sets for the lichen *Cladonia grayi* and its photobiont *Asterochloris sp.*

### 01-assemble

Contains the configuration files for the different assemblers evaluated and also the scripts necessary for preprocessing the data where needed. 

### 02-quast-chimeras

The scripts for analysing the resulting assemblies and scanning for chimeric contigs.