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...ze, 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 produced by...he statistics that we think will be useful for this task. However, nanopore sequencing is an emerging and rapidly de...2407 days ago
coursera genome assembly tutorial
Solutions to Coursera Genome Sequencing (Bioinformatics II)2405 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...2403 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wiki...d or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.An updated version call...2403 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.2403 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...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 pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopo...2401 days ago
Computational Genomics: Applied Comparative Genomics
The primary goal of the course is for students to be grounded in theory and leave the co...uantitative approaches for comparing and analyzing genomes starting from raw sequencing data. The course will focus o...2401 days ago
MinION_GC: An R script to do some QC on MinION data
Other tools focus on getting data out of the fastq or fast5 files, which is slow and computationally intensive. The benefit of this approach is that it works on a single,...2396 days ago