Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
...go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fa...2362 days ago
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TULIP - The Uncorrected Long read Itegration Pipeline
...ended as prototypes, and additional components and/or implementations are likely to follow. Tulipseed takes as input alignments files of long reads to sparse short seeds, and ou...2352 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 dataset o...2352 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...novo assembler for noisy long reads. It takes all-vs-all read sel...r rate is similar to the raw input reads. So far miniasm is in early...m finishes the assembly, including reads overlapping, in ~10 minutes w...ong contigs from raw PacBio or ONT reads without error correction. It...2348 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
...package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predic...e Bayes classifier, RITA is able to achieve very high accuracy on short reads. Unlike other hybrid approach...2348 days ago
Opera: An optimal genome scaffolding program
...i/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads.An updated version called OPE...2348 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.2348 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...ttps://github.com/jgurtowski/nanocorr) specifically for Oxford Nanopore reads, as existing packages were in...ethod we were able to perform a hybrid error correction of the nanopore reads using complementary MiSeq dat...2346 days ago