https://github.com/k8hertweck/asparagalestescripts

brute force approach to TE characterization in non-model systems
https://github.com/k8hertweck/asparagalestescripts

Last synced: 4 days ago
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brute force approach to TE characterization in non-model systems

• Host: GitHub
• URL: https://github.com/k8hertweck/asparagalestescripts
• Owner: k8hertweck
• Created: 2012-12-11T15:11:48.000Z (almost 12 years ago)
• Default Branch: master
• Last Pushed: 2015-04-27T21:23:07.000Z (over 9 years ago)
• Last Synced: 2023-04-04T08:51:57.591Z (over 1 year ago)
• Language: Shell
• Homepage:
• Size: 152 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
AsparagalesTEscripts

====================

Methods from characterization of TEs from low-coverage genome survey sequences in exemplar Asparagales taxa, from [Hertweck 2013](http://www.nrcresearchpress.com/doi/abs/10.1139/gen-2013-0042). This repository is kept as a part of this publication; see other repos for updates to these methods.

**Dependencies:**

* MSR-CA (Maryland Short Read Assembler, now MaSuRCA)

* smalt

* samtools

* seqtk

* cdbyank/cdbfasta

* RepeatMasker

**REpipeline.sh** runs MSR-CA, maps reads to contigs, filters out organellar contigs, runs RepeatMasker on remaining contigs, and summarizes results.

**REDNAsuperfam.sh** parses results further into DNA transposon superfamilies.