Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave the cours...nal and quantitative approaches for comparing and analyzing genomes starting from raw sequencing...2401 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, s...2399 days ago
dnaPipeTE: de-novo assembly & annotation Pipeline for Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small...2397 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that reflect...to collect reads from the metagenome using a simulation of a number of different sequencing...2396 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...2394 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.2385 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific features of O...nd allows for adjustments upon improvement of nanopore seque...tes a set of read profiles serving as the input to the next step,...2382 days ago
dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes.
While the number of sequenced diploid genomes have been steadily increasing in the last few years, assembl...result, there is a shortage of tools for assembling HP genomes from the next generation sequencing (NGS) data...2379 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 hybrid k-mer/read-based assembler that capitalizes on the high accuracy of...2379 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...2378 days ago