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

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