1992 days ago
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 the hood, SvABA uses a custom implement...very 25kb window (with some small overlap) for every region in the genome....1992 days ago
Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF...by Prokka (Seemann, 2014)) and calculates the pan genome. Using a standard desktop PC,...nomics or for comparing extremely diverse sets of genomes...1991 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 sev...our pipeline in both bacterial and eukaryotic genome assemblies, and highlight sev...al assembly errors in both draft and finished genomes...1987 days ago
1914 days ago
1910 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. bioRxiv 2019. RaGOO is a tool for coalescing genome...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 that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes...1877 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.1875 days ago
geck: trio-based comparative benchmarking of variant calls
Determine the accuracy of our model by comparing the precision and recall of GATK Unified Genotyper and Haplotype C...h-confidence SNPs of the NIST Ashkenazim trio and the two independent Platinum Genome...1874 days ago