Table 2.
Haplotype calling software tools for viral NGS data
| Haplotyping tools | Year | System | De novo/Ref based | Pair-end reads | Sequencing error handling | Haplotype assembly method | Haplotype frequency estimation method | Output sequences | Tool availability |
|---|---|---|---|---|---|---|---|---|---|
| Shorah [82] | 2011 | Linux | Ref | + | Probabilistic clustering | Minimal path cover | EM | Full haplotypes | https://github.com/cbg-ethz/shorah |
| ViSpA [60] | 2011 | Linux | Ref | − | Binomial model | Max-bandwidth path | EM | Full haplotypes | http://alan.cs.gsu.edu/NGS/?q=content/vispa |
| QColors [86] | 2012 | — | De novo | − | — | Overlap graph + Conflict graph | — | Full haplotypes | — |
| QuRe [87] | 2012 | Java | Ref | + | Poison model | Multinomial distribution matching | Read coverage | Full haplotypes | https://sourceforge.net/projects/qure/ |
| bioa [85] | 2012 | Linux | Ref | − | k-mer-based error correction | Maximum Bandwidth Path | Fork balancing | Full haplotypes | http://alan.cs.gsu.edu/vira/index.html |
| Vicuna [63] | 2012 | Linux | De novo | + | Read count | — | — | Consensus + contigs | https://www.broadinstitute.org/viral-genomics/vicuna |
| QuasiRecomb [95] | 2013 | Linux | Ref | + | Hidden Markov model | Hidden Markov model | Hidden Markov model | Full haplotypes | https://github.com/cbg-ethz/QuasiRecomb |
| Vira (AmpMCF) [88] | 2013 | Linux | Ref | − | — | Multicommodity flows | Normalized flow size | Full haplotypes | http://alan.cs.gsu.edu/vira/index.html |
| ShotMCF [88] | 2013 | JAVA | Ref | − | Binomial model | Max-bandwidth path + Multicommodity flows | EM + normalized flow size | Full haplotypes | http://alan.cs.gsu.edu/NGS/?q=content/shotmcf |
| BAsE-Seq [61] | 2014 | − | Ref | + | Poisson binomial distribution model | Clustering of reads by SNVs | Read coverage | Full haplotypes | — |
| VGA [90] | 2014 | Linux | Ref | + | Requires high-fidelity sequencing protocol | Min-graph coloring | EM | Full haplotypes | http://genetics.cs.ucla.edu/vga/ |
| HaploClique [89] | 2014 | Linux | Ref | + | — | Max-clique enumeration | Normalized read count | Full haplotypes | https://github.com/cbg-ethz/haploclique |
| PredictHaplo [96] | 2014 | Linux | Ref | + | Dirichlet Process Mixture Model | Dirichlet Process Mixture Model | Dirichlet Process Mixture Model | Full haplotypes | https://bmda.dmi.unibas.ch/software.html |
| IVA [64] | 2015 | Linux | De novo | − | Read count | — | — | Contigs | https://sanger-pathogens.github.io/iva/ |
| MLEHaplo [98] | 2015 | Linux | De novo | + | — | Maximum likelihood | — | Full haplotypes | https://github.com/raunaq-m/MLEHaplo |
| ViQuaS [91] | 2015 | Linux | Ref | + | Chimeric error correction | Multinomial distribution matching | Read count | Full haplotypes | https://sourceforge.net/projects/viquas/ |
| SAVAGE [65] | 2017 | Linux | De novo | + | Overlap fuzzy matching error correction | Enumerating cliques in overlap graph | EM | Contigs | https://bitbucket.org/jbaaijens/savage/ |
| aBayesQR [100] | 2017 | Linux | Ref | + | Cluster coverage by reads | Bayesian inference | Bayesian inference | Full haplotypes | https://github.com/SoYeonA/aBayesQR |
| RegressHaplo [97] | 2017 | R | Ref | + | — | Penalized regression | Penalized regression | Full haplotypes | https://github.com/SLeviyang/RegressHaplo |
| 2SNV [99] | 2017 | Java | Ref | − | Linkage of SNV pairs | Hierarchical clustering of reads by SNVs | EM | Full haplotypes | http://alan.cs.gsu.edu/NGS/?q=content/2snv |
| PEHaplo [92] | 2018 | Linux | De novo | + | Overlap error correction | Path finding in overlap graph | — | Contigs | https://github.com/chjiao/PEHaplo |
| Shiver [66] | 2018 | Linux | De novo + ref | + | BLAST database match | — | — | Consensus | https://github.com/ChrisHIV/shiver |
| CliqueSNV [76] | 2018 | JAVA | Ref | + | Linkage of SNV pairs | Clique enumeration and merging | EM | Full haplotypes | https://github.com/vtsyvina/CliqueSNV |