Results for "read depth"
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Meraculous: De Novo Genome Assembly with Short Paired-End Reads
We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megaba...or correction step as used in other short-read...2387 days ago
QuorUM: An Error Corrector for Illumina Reads
Illumina Sequencing data can provide high coverage of a genome b...(most often 100 bp to 150 bp) reads at a low cost. Even with low...average has an error in some read at every base in the genome....erroneous k-mers in the reads. However, there is enough in...at error correcting Illumina reads...2385 days ago
Unicycler: Hybrid assembly pipeline for bacterial genomes
Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or&nbs...ossible assemblies, give it both Illumina reads...2384 days ago
- DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads. The number of input read sets is not constrained, it can be one, two, or more. No reference genome is needed.
2374 days ago
TULIP - The Uncorrected Long read Itegration Pipeline
#Running TULIP (The Uncorrected Long-read Integration Process), version 0.4 late 2016 (Europ...;Tulipseed takes as input alignments files of long reads to sparse short seeds, and o...graph and scaffold structures. Tulipbulb adds long read...2371 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&n...simply concatenates pieces of read sequences to generate the fin...ishes the assembly, including reads overlapping, in ~10 minutes...ontigs from raw PacBio or ONT reads...2367 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wi...nbsp;). It uses information from paired-end or long reads to optimally order and orient contigs assembled from shotgun-sequencing reads...2367 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...corr) specifically for Oxford Nanopore reads, as existing packages were incapable of assembling the long read lengths (5-50kbp) at such hig...e, the assembly with the long nanopore reads...2365 days ago
- Computational Biology is a huge field of study, that touches upon many d...indexing and exact search Heuristics for read alignment and ...mapping &mdash mapping DNA-seq and RNA-seq reads...
2365 days ago
Musket: a multistage k-mer spectrum based corrector
Musket is a well-established leading next-generation sequencing read error correction algorithm targetting Illumina sequencing. This corre...g substitution-error-based correctors. In addition, Musket is multi-threade...2358 days ago
