2017 days ago
Biotite: A general framework for computational biology
The package is open source and freely available at...d structure modules serve for the analysis of sequence and structural data analysis respectively, database&n...data and supports various file formats and analysis and manipulation functions....2017 days ago
Versatile genome assembly evaluation with QUAST-LG
QUAST-LG is an extension of QUAST intended for evaluating large-scale genom...completeness and correctness metrics BUSCO added for enhanced reference-free analysis The concept of upper bound&n...2013 days ago
2004 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...1999 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 b...assembly starting with data quality control, through to building contigs and analysis of the results. At the end of...1984 days ago
Roary: the Pan Genome Pipeline
Roary is a high speed stand alone pan genome pipeline, which takes annotated assembli...sed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would...1982 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 polyploidiza...ploids, triploids and tetraploids, on the basis of frequency distributions at variant...1973 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 re...orienting of contigs. Chimeric contig correction GFF lift-over Structural variant...1896 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 Caller on the high-confidence SNPs of the NIST Ashkenaz...1864 days ago