Ispecies assembly strongly, but sometimes higher coverage led to decreased performance, for example, for read length of 150 bases and error rate 0.01 in 
the high-diversity dataset, reflecting the limitations of global haplotype reconstruction (rows of Figures 2 and 3). By contrast, the read length has a strong impact on the inference of long haplotypes (columns of Figures 2 and 3). Even with a high level of diversity, 36 bases long reads are insufficient to infer haplotypes on a 252 bp long region reliably, regardless of the noise level or the coverage. However, the performance improves significantly when increasing the read length to 75 bases, and with the current reads of 150 bases, the haplotypes can be reconstructed with good accuracy between 60 and 100 , provided that MedChemExpress AKT inhibitor 2 errors are infrequent. A high error rate will decrease the reconstruction quality significantly, especially for longer reads of 75 and 150 bp.DiscussionWe have presented a comparison of two sequencing platforms for the study of viral diversity highlighting the trade-offs between sequencing depth, sequencing errors, and read length. If the analysis is focused on a local region of the genome covered by the reads, then Illumina’s higher accuracy and higher throughput enabling deep coverage are advantageous with respect to 454/ Roche. In this case, haplotype reconstruction is both more sensitive and more specific for Illumina data. On the other hand,read length has a tremendous impact when one tries to match the diversity detected at sites more distant than the read length, and in this case, the 454/Roche platform has a clear advantage. Even the experimental Illumina datasets obtained from the highly diverse population analyzed here, do not allow for reliable reconstruction of the haplotypes. For example, with 36 bp long reads, regardless of the coverage and even assuming a low error rate, one can hardly reconstruct 50 of the population reliably (Figure 2). Thus, for long-range haplotype reconstruction in clinical samples, which often will display less diversity, read length appears to be the 
most critical factor. Although both NGS technologies analyzed here have been improving rapidly in the last few years, their main distinctions remain. 454/Roche is still characterized by a higher indel error rate in homopolymeric regions. Illumina has a smaller total error rate, and a lower cost per GNF-7 cost sequenced base [31]. Both platforms increased their read length, with 454 now generating reads of average length 800 bp and Illumina of 150 bp, but their relative advantages and disadvantages are virtually unaltered. Of course, the performance of either platform can be boosted by increasing the coverage, but the sequencing error patterns remain a limiting factor. Importantly, increasing coverage is more cost-effective and less labor-intensive with Illumina than with 454/Roche. To compare the relatively long-read 454/Roche sequencing platform with the short-read Illumina technology, we have considered a genomic region covered entirely by the long readsViral Quasispecies Reconstructionbut not by the short reads. Since a head-to-head comparison is not possible, we have explored two approaches. First, we defined a local window of maximal average entropy in the hope of detecting the population diversity with local reconstruction methods from short reads there. This approach is particularly useful for diverse populations and although it will not result in the set of global haplotypes, it can b.Ispecies assembly strongly, but sometimes higher coverage led to decreased performance, for example, for read length of 150 bases and error rate 0.01 in the high-diversity dataset, reflecting the limitations of global haplotype reconstruction (rows of Figures 2 and 3). By contrast, the read length has a strong impact on the inference of long haplotypes (columns of Figures 2 and 3). Even with a high level of diversity, 36 bases long reads are insufficient to infer haplotypes on a 252 bp long region reliably, regardless of the noise level or the coverage. However, the performance improves significantly when increasing the read length to 75 bases, and with the current reads of 150 bases, the haplotypes can be reconstructed with good accuracy between 60 and 100 , provided that errors are infrequent. A high error rate will decrease the reconstruction quality significantly, especially for longer reads of 75 and 150 bp.DiscussionWe have presented a comparison of two sequencing platforms for the study of viral diversity highlighting the trade-offs between sequencing depth, sequencing errors, and read length. If the analysis is focused on a local region of the genome covered by the reads, then Illumina’s higher accuracy and higher throughput enabling deep coverage are advantageous with respect to 454/ Roche. In this case, haplotype reconstruction is both more sensitive and more specific for Illumina data. On the other hand,read length has a tremendous impact when one tries to match the diversity detected at sites more distant than the read length, and in this case, the 454/Roche platform has a clear advantage. Even the experimental Illumina datasets obtained from the highly diverse population analyzed here, do not allow for reliable reconstruction of the haplotypes. For example, with 36 bp long reads, regardless of the coverage and even assuming a low error rate, one can hardly reconstruct 50 of the population reliably (Figure 2). Thus, for long-range haplotype reconstruction in clinical samples, which often will display less diversity, read length appears to be the most critical factor. Although both NGS technologies analyzed here have been improving rapidly in the last few years, their main distinctions remain. 454/Roche is still characterized by a higher indel error rate in homopolymeric regions. Illumina has a smaller total error rate, and a lower cost per sequenced base [31]. Both platforms increased their read length, with 454 now generating reads of average length 800 bp and Illumina of 150 bp, but their relative advantages and disadvantages are virtually unaltered. Of course, the performance of either platform can be boosted by increasing the coverage, but the sequencing error patterns remain a limiting factor. Importantly, increasing coverage is more cost-effective and less labor-intensive with Illumina than with 454/Roche. To compare the relatively long-read 454/Roche sequencing platform with the short-read Illumina technology, we have considered a genomic region covered entirely by the long readsViral Quasispecies Reconstructionbut not by the short reads. Since a head-to-head comparison is not possible, we have explored two approaches. First, we defined a local window of maximal average entropy in the hope of detecting the population diversity with local reconstruction methods from short reads there. This approach is particularly useful for diverse populations and although it will not result in the set of global haplotypes, it can b.
