Referee: Genome assembly quality scores
...ore for each position in the genome assembly. We accomplish this by first calculating genotype likelihoods for every site. For a given site in a diploid genome, there are 10 possible...2022 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
...or downstream analysis whether you're working on the haploid or phased-diploid assembly. Identify pairs of...bly (i.e. Canu, FALCON or FALCON-Unzip primary contigs) or on a phased-diploid assembly (i.e. FALCON-Unzip p...1980 days ago
Tadpole: an assembler, error-corrector, and read-extender
...f error-correcting and extending reads. It does not do any complicated graph analysis or scaffolding, and therefore, is not particularly good for diploid organisms. Tadpole is ve...1565 days ago
1300 days ago
GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.
...al link based on overlaps, it yields high-quality gap-less supercontigs. To demonstrate the efficiency of GraphUnzip, we tested it on a simulated diploid Escherichia coli genome, and...1198 days ago
Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency...1057 days ago