EGAD: Ultra-fast functional analysis of gene networks
With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in netwo...2032 days ago
Purge Haplotigs: Pipeline to help with curating heterozygous diploid genome assemblies
Some parts of a genome may have a very high degree of heterozygosity. This causes...an as a contig and an associated haplotig. This can be an issue for downstream analysis whether you're working on the...2029 days ago
2028 days ago
Biotite: A general framework for computational biology
The package is open source and freely available...nd structure modules serve for the analysis of sequence and structural data analysis respectively, database&n...e data and supports various file formats and analysis and manipulation functions.2028 days ago
Versatile genome assembly evaluation with QUAST-LG
QUAST-LG is an extension of QUAST intended for evaluating large-scale ge...completeness and correctness metrics BUSCO added for enhanced reference-free analysis The concept of upper bound&n...2024 days ago
2015 days ago
ZENBU: a collaborative, omics data integration and interactive visualization system
ZENBU is a data integration, data analysis, and visualization system enhanced for RNAseq, ChipSeq, CAGE and other types of next-generation-sequence-tag (NGS) based data. ZENBU allows for nove...2011 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 wil...e assembly starting with data quality control, through to building contigs and analysis of the results. At the end of...1995 days ago
Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assem...ysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would...1993 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is ob...1984 days ago