github.com - GFA (Graphical Fragment Assembly) is an emerging standard format for representing sequence graphs. Although it was originally conceived as a format for sequence assembly (hence the name), and this remains its core application, it is more general,...
csb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...
github.com - RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types:
single-end/paired-end bulk RNA-seq (strand-specific/agnostic)
paired-end single-cell RNA-seq...
help.rc.ufl.edu - More at https://help.rc.ufl.edu/doc/Kmer
This also includes:
A2Amapper: ATAC, Assembly to Assembly Comparision tool:
Comparative mapping between two genome assemblies (same species), or between two different genomes (cross...
github.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...
ancestralgenomes.org - Ancestral Genomes (http://ancestralgenomes.org) is a resource for comprehensive reconstructions of these ‘fossil genomes’. Comprehensive sets of protein-coding genes have been reconstructed for 78 genomes of now-extinct species...
They are based in the Department of Genetics at the University of Cambridge.
The research covers diverse areas of evolutionary biology, and molecular evolution in particular. It combines theoretical and empirical approaches, and particularly...
Air date: Wednesday, January 04, 2012, 3:00:00 PM
Time displayed is Eastern Time, Washington DC Local
Category: Wednesday Afternoon Lectures
Description: There is a broad consensus that cancer is the result of somatic cells having serially...
Broad area of research:
Genome Annotation and Functional Genomics
Bergman Lab is actively engaged in the development and application of computational methods to improve the annotation of functional biological features in genome sequences....
The premise of Assassin's Creed is the reliving of other people's memories stored inside DNA. Well scientists have found that in mice, it actually happens! Anthony is joined by special guest and our friend Tara Long from Hard Science to explain how...