RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
...r UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to achieve very high accuracy on short reads. Unlike other hybrid approaches which combine thes...2378 days ago
Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
...iae genome. To make use of these data, we developed a novel open-source hybrid error correction algorithm Na...tween ~5 and 40% error). With this new method we were able to perform a hybrid error correction of the nanop...2376 days ago
Meraculous: Haplotype-sensitive Assembly of Highly Heterozygous genomes.
Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes. It is a hybrid k-mer/read-based assembler that capitalizes on the high accuracy of...2354 days ago
Jabba: Hybrid Error Correction for Long Sequencing Reads
Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data. Input Jabba takes as input a c...2008 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82224 days ago
Cerulean: A hybrid assembly using high throughput short and long reads
...nted with bacterial genomes in mind. The method is fully described in Deshpande, V., Fung, E. D., Pham, S., & Bafna, V. (2013). Cerulean: A hybrid assembly using high throughpu...2188 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the...2121 days ago
Hercules: a profile HMM-based hybrid error correction algorithm for long reads
Choosing whether to use second or third generation sequencing platforms can lead to trade-offs between accuracy and read length. Several studies require long and accura...2111 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...of coverage. This motivates the development of hybrid approaches that leverage the...errors in long reads.We introduce CoLoRMap, a hybrid method for correcting noisy l...show that CoLoRMap compares well with existing hybrid correction methods.The source...2111 days ago
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decis...1977 days ago