Volume 1 I have chosen two examples, contingency table analysis and causal inference, but I could have written similarly about the evolution of statistical thinking associated with time series analysis, again going back to early contributions of Yule), or about spatial statistics or meta-analysis. Over time, we hope to provide comprehensive reviews Read more…
GAML: genome assembly by maximum likelihood (2015) Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling (2014) ILP-based maximum likelihood genome scaffolding (2014) Toward a statistically explicit understanding of de novo sequence assembly (2013) CGAL: computing genome assembly likelihoods (2013) Denovo likelihood-based measures for comparing genome assemblies (2013) ALE: a generic assembly likelihood Read more…
GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or long-read alignments (2015) Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology (2012) (PBJelly)
ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter (2017) departs from MPI and instead implements algorithms that employ a Bloom filter, a probabilistic data structure, to represent a de Bruijn graph and reduce memory requirements. We benchmarked ABySS 2.0 human genome assembly using a Genome in a Read more…
A comparative evaluation of genome assembly reconciliation tools (2017) benchmarked seven assembly reconciliation tools, namely CISA, GAA, GAM_NGS, GARM, Metassembler, MIX, and ZORRO Despite the inability of these assembly tools to solve the general assembly reconciliation problem, each tool demonstrated some strengths that could lead to algorithmic advances for this problem. For instance, CISA generally was Read more…