Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
Modern genome sequencing strategies are highly sensitive to contamin...st, a simple pipeline with a graphical user interface, for th...e based on multiple blastn searches with short sequence fragm...ata to public repositories. Our analysis pipeline is open-sou...2419 days ago
TULIP - The Uncorrected Long read Itegration Pipeline
#Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (European eel) TULIP currently consists of to Perl scripts, tulipseed.perl and...itional components and/or implementations are likely to follow. Tulip...2419 days ago
poRe: an R package for the visualization and analysis of nanopore sequencing data
Motivation: The Oxford Nanopore MinION device represents a u...hese applications, the bioinformatics community will need to...to manipulate, organize, summarize and visualize MinION nanop...lable at https://sourceforge.net/p/rpore/wiki/Home/ Con...2419 days ago
ONT assembly and Illumina polishing pipeline
This pipeline performs the following steps: Assembly of nanopore reads using Canu. Polish canu contigs using racon (optional). Map a paired-end Illumina da...in the previous steps using BWA mem. Perform correction of contigs usi...2419 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 Oxford Nanopore&rsquo...It includes a functions to generate a number plots for examini...ping technology. It is not clear what will be most informative...traight to the getting FASTQ format files from fast5 files you...2419 days ago
SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
This is the c++ implementation for SIMA - Simultaneous Multiple Alignmen...Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various ope...tu 10.10 64bit, and gentoo AMD64. The corresponding publication can be...2419 days ago
coursera genome assembly tutorial
Solutions to Coursera Genome Sequencing (Bioinformatics II)2417 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...eces of read sequences to generate the final unitig ...HGAP3 assembly (on Y). They are broadly comparable. Of cours...Install minimap and miniasm (requiring gcc and zlib) git cl...2415 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology pr...ompositional classifications from a Naive Bayes classifier, R...ccepted to Nucleic Acids Research April 4, 2012. I...2415 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/w...ce_assembly ). It uses information from paired-end or long...n-sequencing reads.An updated version called OPERA-LG has been...-rich eukaryotic genomes with performance guarantees. Genome Bi...2415 days ago