Graph-based reference genomesHaplotype-aware graph indexesRead alignmentThe practical use of graph-based reference genomes depends on the ability to align reads to them. Performing substring queries to paths through these graphs lies at the core of this task. The combination of increasing pattern ...
Heller, D., Vingron, M., Church, G., Li, H. & Garg, S. SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing. bioRxiv 2020.02.25.964445 (2020) doi:https://doi.org/10.1101/2020.02.25.964445. Koren S, ...
ALLHiC is a widely used allele-aware scaffolding tool designed for this purpose. However, its dependence on chromosome-level reference genomes and a higher chromosome misassignment rate still impede the unravelling of haplotype-resolved genomes. Here we present HapHiC, a reference-independent allele-...
For the second modality of variant-aware isoform detection, since we anticipated working with RNA edits and potential cancer-related aneuploidies that may result in more than two consistent haplotypes, FLAIR2 can approach phasing variants in a manner that is agnostic to ploidy: (1) from the isofo...
one per region, and run them on a cluster. Be aware that the freebayes-parallel script contains calls to other programs using relative paths from the scripts subdirectory; the easiest way to ensure a successful run is to invoke the freebayes-parallel script from within the scripts subdirectory....