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. 2021 Jul 19;22(1):212.
doi: 10.1186/s13059-021-02426-8.

Haploflow: strain-resolved de novo assembly of viral genomes

Adrian Fritz  1   2 , Andreas Bremges  1   2 , Zhi-Luo Deng  1 , Till Robin Lesker  1   2 , Jasper Götting  2   3 , Tina Ganzenmueller  2   3   4 , Alexander Sczyrba  1   5 , Alexander Dilthey  6   7 , Frank Klawonn  8   9 , Alice Carolyn McHardy  10   11
Affiliations

Haploflow: strain-resolved de novo assembly of viral genomes

Adrian Fritz et al. Genome Biol. .
No abstract available

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Flow chart of the Haploflow algorithm and its two parts: First, the construction of the deBruijn graph and operations thereon, namely splitting it by connected components and calculating coverages. Then, the creation of the unitig graphs per CC and the assembly process consisting of calculating the thresholds and the coverage histograms and the putative paths through the graphs. Next is the calculation of the concrete flows and thereby the generation of the contigs and finally the cleaning of the graph and the generation of the assembly graphs. As intermediate output, the assembly graph is created during every step (bottom left)
Fig. 2
Fig. 2
The adapted Dijkstra algorithm used in Haploflow to find fattest paths through the unitig graph. Instead of determining the shortest paths from the source to all vertices, this algorithm determines the fattest path. The fatness is initialized as 0 for all vertices, but the source and then the graph is searched using a breadth-first search and based on the fact that the fattest path from a source s to a sink t is based on the edge with the lowest coverage along this path (lines 9 to 12)
Fig. 3
Fig. 3
Phylogenetic relationships of reconstructed strain genomes inferred with Raxml [40, 41], including closely related (ANI greater than 99.99%, determined with MASH [42]) strains from GISAID [43]. Strains from the same sample are indicated by color, and “major” and “minor,” based on their inferred abundances. Evolutionary events, including mutations, and indels are shown on edges
Fig. 4
Fig. 4
A HIV genome structure [60] and Icarus plots [61] for three HIV strains reconstructed by Haploflow. For each of the three reference genomes, there is one contig spanning almost the complete genome. B Radar plot of relative performance with commonly used and strain-resolved genome assembly metrics for Haploflow and 12 other methods on the HCMV benchmark data (best values are at 100%, see the “Performance evaluation” section). Haploflow, in orange, ranks first in genome fraction, strain recall, strain precision, and composite score. C Boxplots with median and interquartile range of genome fraction and NGA50 values across samples for different methods
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