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https://github.com/cbg-ethz/5-virus-mix

Benchmarking data sets for haplotype reconstruction methods, sequenced with Illumina MiSeq, 454/Roche GSJunior, and Pacific Biosciences

https://github.com/cbg-ethz/5-virus-mix

Science Score: 23.0%

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    CITATION.cff file
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    .zenodo.json file
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    DOI references
    Found 1 DOI reference(s) in README
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    Academic publication links
    Links to: ncbi.nlm.nih.gov
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    Scientific vocabulary similarity
    Low similarity (5.5%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Benchmarking data sets for haplotype reconstruction methods, sequenced with Illumina MiSeq, 454/Roche GSJunior, and Pacific Biosciences

Basic Info
  • Host: GitHub
  • Owner: cbg-ethz
  • Default Branch: master
  • Size: 191 KB
Statistics
  • Stars: 22
  • Watchers: 9
  • Forks: 4
  • Open Issues: 1
  • Releases: 0
Created about 12 years ago · Last pushed over 6 years ago
Metadata Files
Readme

README.md

5-virus-mix

Dr. Armin Töpfer, armintoepfer.com

HIV-1 full-length benchmarking data sets for haplotype reconstruction methods, sequenced with Illumina MiSeq, 454/Roche GSJunior, and Pacific Biosciences. Five well-studied HIV-1 strains (HXB2, 89.6, JR-CSF, NL4-3, and YU-2) have been mixed and sequenced. Individual strains have also been resequenced to validate reconstruction results.

Citation

If you use this data, please cite:
Di Giallonardo, Töpfer et al.
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations
NAR, 2014 10.1093/nar/gku537

Lab workflow

HaploClique

Data sets

Illumina.sra
454.sra
PacBio.sra

True haplotypes

Reconstructed haplotypes

These haplotypes have been reconstructed with respect to the HXB2 reference space, excluding insertion: 5VM.fasta

Resequenced references

Resequenced full-length references: REF.fasta

Contact

For questions regarding analysis of the data:
armin.toepfer (at) gmail.com

Owner

  • Name: Computational Biology Group (CBG)
  • Login: cbg-ethz
  • Kind: organization
  • Location: Basel, Switzerland

Beerenwinkel Lab at ETH Zurich

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 13
  • Total Committers: 1
  • Avg Commits per committer: 13.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Armin Töpfer a****r@g****m 13

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: 18 days
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 0.67
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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  • AntonCoon (1)
  • sekhwal (1)
  • ekg (1)
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