Genome-wide somatic variant calling using localized colored de Bruijn graphs
Sign Up to like & getrecommendations! Published in 2018 at "Communications Biology"
DOI: 10.1038/s42003-018-0023-9
Abstract: Reliable detection of somatic variations is of critical importance in cancer research. Here we present Lancet, an accurate and sensitive somatic variant caller, which detects SNVs and indels by jointly analyzing reads from tumor and… read more here.
Keywords: colored bruijn; genome wide; variant; lancet ... See more keywords
Succinct Dynamic de Bruijn Graphs.
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btaa546
Abstract: MOTIVATION The de Bruijn graph is one of the fundamental data structures for analysis of high throughput sequencing data. In order to be applicable to population-scale studies, it is essential to build and store the… read more here.
Keywords: addition; succinct dynamic; graph; bruijn ... See more keywords
Accurate self-correction of errors in long reads using de Bruijn graphs
Sign Up to like & getrecommendations! Published in 2017 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btw321
Abstract: Motivation: New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50 000 bp long but with an error rate of at least 15%. Reducing the error rate… read more here.
Keywords: long reads; bruijn graphs; correction; method ... See more keywords
Simplitigs as an efficient and scalable representation of de Bruijn graphs
Sign Up to like & getrecommendations! Published in 2021 at "Genome Biology"
DOI: 10.1186/s13059-021-02297-z
Abstract: de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their computation.… read more here.
Keywords: scalable representation; bruijn graphs; efficient scalable; representation ... See more keywords