Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave the course empowered to...ing genomes starting from raw sequencing data. The course will focus on human genomics and h...on, personal genome analysis, and cancer genomics. The grading will be...2404 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic read...ifferent levels of the NCBI taxonomy, and then to collect reads from th...p;simulation of a number of different seque...ved sequences based on source genomes and a given evolutionary tree.2398 days ago
Musket: a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction...algorithm targetting Illumina sequencing. This corrector employ...n terms of correction quality and de novo genome assembly measures, re...ed using a master-slave model and demonstrates superior parallel scala...2397 days ago
SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.2388 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the te...-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first...nsive alignment-based analysis and g.... NanoSim is written in Python and R. The source files and manual are a...2385 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in the la...for assembling HP genomes from the next generation seque...embling HP genomes were proposed in the pre-NGS era and are not well suited for NGS projects...2382 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a...asets by utilizing lightweight data structures and m...ocess pipeline implements a highly transparent and portable model of job control and mo...2382 days ago
AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standar...en combined to conventional public pipelines and ∼48% to the in-house commercial...2381 days ago
2376 days ago
Ra assembler - a de novo DNA assembler for third generation sequencing data
Integration of the Ra assembler - a de novo DNA assembler for third generation sequencing data developed on Faculty of Electrical Engineering and Computing (FER), Ruder Boskovic Institute (RBI) and G...ng overlaps using a very sensitive and specific overlapper ("graphmap -w ow...2375 days ago