RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bi...1667 days ago
MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
...samples from WT mice or mice lacking a single TF in a particular neuronal subtype 4) Single cell RNAseq analysis of neurons divided by Immediate Early Gene expression levels. In...1270 days ago
GraphUnzip: Phases an assembly graph using Hi-C data and/or long reads.
...a and the potato Solanum tuberosum. In all cases, GraphUnzip yielded highly continuous phased assemblies. https://www.biorxiv.org/content/biorxiv/early/2021/02/01/2021.01.29.428779....1199 days ago
Calling variants in non-diploid systems
...ling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have...1058 days ago
k-mers tutorial - classification and taxonomy
DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently,&nbs...997 days ago