EGAD: Ultra-fast functional analysis of gene networks
With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we pr...guilt-by-association principle. These allow rapid controlled comparisons and analyses. Two of the core features are...2031 days ago
ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic hapl...C scaffolding pipeline, called ALLHIC, specifically tailored to the polyploid genomes....2024 days ago
EXCAVATOR: detecting copy number variants from whole-exome sequencing data
EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequenci...TOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperfor...2010 days ago
2003 days ago
Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by...is not intended for meta-genomics or for comparing extremely diverse sets of genomes....1992 days ago
Genome assembly forensics: finding the elusive mis-assembly
We present the first collection of tools aimed at automated genome assembly validation. This work formalizes severa...assemblies, and highlight several assembly errors in both draft and finished genomes....1987 days ago
OMTools: a software package for visualizing and processing optical mapping data
OMTools, an efficient and intuitive data processing and visualization suite to handle...dules together form an accessible and convenient pipeline for optical mapping analyses. https://github.com/TF-Chan-...1926 days ago
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....1906 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver tha...t invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes....1878 days ago
gEVAL: Genome Evaluation Browser
...the evaluation of genome assemblies through its tools and pre-computed analyses. The strength of this brows...l assemblies to a “gold” standard for release as reference genomes1845 days ago