Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we us...2369 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs...2365 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequenc...2363 days ago
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 conduct independent genomic analyses. We will study the lead...2363 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, su...2361 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a...2358 days ago
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
An efficient tool called Connecting Overlapped Pair-End (COPE) reads, to connect overlapping pair-end reads using k-mer frequencies. We evaluated our tool on 30× sim...2356 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 employs the k-mer...2356 days ago
jobTree based python wrapper to run the genome simulation tool suite Evolver
evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver,&nb...2353 days ago
Mugsy: multiple whole genome alignment tool
Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the...2353 days ago