Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Unlike EULER and similar progams, Quake utilizes a robust mixture model of erroneous and genuine k-mer distributions to determine where errors are located. Then Quake uses read quality values and learns the nucleotide to nucleotide error rates to determine what types of errors are most likely. This leads to more corrections and greater accuracy, especially with respect to avoiding mis-corrections, which create false sequence unsimilar to anything in the original genome sequence from which the read was taken.
Keywords for this software
References in zbMATH (referenced in 5 articles )
Showing results 1 to 5 of 5.
- Pellegrina, Leonardo; Pizzi, Cinzia; Vandin, Fabio: Fast approximation of frequent (k)-mers and applications to metagenomics (2019)
- Schulz, Marcel H.; Bar-Joseph, Ziv: Probabilistic models for error correction of nonuniform sequencing data (2017)
- Weese, David; Schulz, Marcel H.; Richard, Hugues: DNA-seq error correction based on substring indices (2017)
- Daugelaite, Jurate; O’Driscoll, Aisling; Sleator, Roy D.: An overview of multiple sequence alignments and cloud computing in bioinformatics (2013)
- Zhao, Zhiheng; Yin, Jianping; Zhan, Yubin; Xiong, Wei; Li, Yong; Liu, Fayao: PSAEC: an improved algorithm for short read error correction using partial suffix arrays (2011)