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.
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
These haplotypes have been reconstructed with respect to the HXB2 reference space, excluding insertion: 5VM.fasta
Resequenced full-length references: REF.fasta
For questions regarding analysis of the data:
armin.toepfer (at) gmail.com