QuorUM: An Error Corrector for Illumina Reads
Illumina Sequencing data can provide high coverage of a genome by...the genome. These errors make handling the data more complicated...he reads to correct most of the seque...oth changes in individual bases and trimming of unu...ving the most true k-mers, and we introduce a composite statistic &...2421 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
Modern genome sequencing strategies are highly sensitive to contamination making the de...well as hybrid scaffolds that contain both bacterial and a...uration, may thus constitute a useful complement to standard bioinformatics an...2407 days ago
TULIP - The Uncorrected Long read Itegration Pipeline
#Running TULIP (The Uncorrected Long-read Integration Process),...Perl scripts, tulipseed.perl and tulipbulb.perl. These are ver...much intended as prototypes, and additional components and/or...rt seeds, and outputs a graph and s...res. Tulipbulb adds long read sequencing data to these. https...2407 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...community will need to design and b...nipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poR...2407 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 pro...ll be useful for this task. However, nanopore sequencing is an emerging and r...n of metrics that we haven’t thought of, and welcome feedback at mike.smith@...2406 days ago
coursera genome assembly tutorial
Solutions to Coursera Genome Sequencing (Bioinformatics II)2405 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http...paired-end or long reads to optimally order and orient contigs assembled from shotgun-seque...ered with features for the assembly of large and complex genomes.Song Gao, Denis Bert...2402 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.2402 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...rvations only incorporate noise due to sequencing and do not incorporate effects from more.... simNGS takes fasta format sequences and a file describing the covariance of...2402 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 por...en postulated as a method for sequencing DNA for several decade...h high error rate (between ~5 and 40% error). With this new method we...sing complementary MiSeq data and produce a de novo assembly that is h...2401 days ago