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 use Taxo...2404 days ago
TULIP - The Uncorrected Long read Itegration Pipeline
#Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2...t seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these. https...2404 days ago
poRe: an R package for the visualization and analysis of nanopore sequencing data
Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB por...ize, summarize and visualize MinION nanopore sequencing data. As a package for R, poR...2404 days ago
IONiseR: tools for the quality assessment of data produced by Oxford Nanopore’s MinION sequencer
This package is intended to provide tools for the quality assessment of data produ...the statistics that we think will be useful for this task. However, nanopore sequencing is an emerging and rapidly de...2404 days ago
coursera genome assembly tutorial
Solutions to Coursera Genome Sequencing (Bioinformatics II)2402 days ago
Opera: An optimal genome scaffolding program
...ong reads to optimally order and orient contigs assembled from shotgun-sequencing reads.An updated versi...ptimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 201...2400 days ago
INC-Seq: accurate single molecule reads using nanopore sequencing
INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling on the MinION system.2400 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-cal...tware. By default, observations only incorporate noise due to sequencing and do not incorporate effect...2399 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...rane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopo...nome and correctly assembles gene cassettes, rRNAs, transposable elements, and other g...2398 days ago
Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave...quantitative approaches for comparing and analyzing genomes starting from raw sequencing data. The course will focus o...2398 days ago