gVolante: Completeness Assessment of Genome/Transcriptome Sequences
A brand-new web server, gVolante, which provides an online tool for (i) on-demand completeness assessment of sequence sets by means of the previously developed pipelines CEGMA and BUSCO and (ii) browsing pre-computed completeness scores for publicly available data in its database section2002 days ago
LTR_Finder: an efficient program for finding full-length LTR retrotranspsons in genome sequences.
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences. The Program first constructs all exact match pairs by a suffix-array based algorithm and exte...2002 days ago
2002 days ago
Quick tour of Genetic Algorithms !
The R package GA provides a collection of general purpose functions for opt...own objective function depending on the problem at hand. https://cran.r-project.org/web/packages/GA/vignettes...1998 days ago
Genome assembly tutorial "Genome Assembly for short and long reads"
In this lab we will perform de novo genome assembly of a bacterial genome. You will be guided through the genome assembly starting with data quality control, through to building contigs a...1996 days ago
Osprey: Network Visualization System
Osprey is a software platform for the visualization of complex biological interaction networks. Osprey bui...z, BJ., Stark, C., Tyers M. "Osprey: A Network Visualization System." Genome Biology 2003 4(3):R22 [Genome...1995 days ago
1994 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....1994 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...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 sev...our pipeline in both bacterial and eukaryotic genome assemblies, and highlight sev...al assembly errors in both draft and finished genomes...1989 days ago