SvABA: Genome-wide detection of structural variants and indels by local assembly
SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under th...w (with some small overlap) for every region in the genome. The default is to use only c...1994 days ago
Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies i...okka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC,...s or for comparing extremely diverse sets of genomes.1993 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...pipeline in both bacterial and eukaryotic genome assemblies, and highlight sev...ssembly errors in both draft and finished genomes. The software described is c...1989 days ago
1916 days ago
1912 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ,...C: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into pseudoc...1908 days ago
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a through...invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a&nb...1880 days ago
MGERT: Mobile Genetic Elements Retrieving Tool
MGERT is a computational pipeline for easy retrieving of MGE's coding sequences of a particular family from genome assemblies. MGERT utilizes several established bioinformatic tools combined into single pipeline which hides different technical quirks from an inexperienced user.1877 days ago
geck: trio-based comparative benchmarking of variant calls
Determine the accuracy of our model by comparing the precision and recall of GATK U...gh-confidence SNPs of the NIST Ashkenazim trio and the two independent Platinum Genome trios. We show that our metho...1876 days ago
Apollo: First instantaneous, collaborative genomic annotation editor available on the Web
Apollo is a plug-in for the JBrowse Genome Viewer. In addition to genes and pseudogenes, users can annotate ncRNAs (snRNA, snoRNA, tRNA, rRNA), miRNAs, repeat regions, and transpo...1864 days ago