BOL

github.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....

A major breakthrough (replaced microarrays) in the late 00’s and has been widely used since Measures the average expression level for each gene across a large population of input cells Useful for comparative transcriptomics,...

The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods...

github.com -  Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...

Removing contaminated sequences using NCBI quality assurance tools

jgi.doe.gov - Tadpole is a kmer-based assembler, with additional capabilities of 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...

omega.omicsbio.org - Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph...

In graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.

amos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...

bioinfo.konkuk.ac.kr - The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo...