Variable-order reference-free variant discovery with the Burrows-Wheeler Transform

Fully Functional Suffix Trees and Optimal Text Searching in BWT-Runs Bounded Space

(2020) Travis Gagie et al.   JOURNAL OF THE ACM

Best practices for benchmarking germline small-variant calls in human genomes

(2019) Peter Krusche et al.   NATURE BIOTECHNOLOGY

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

(2019) Antoine Limasset et al.   BIOINFORMATICS

External memory BWT and LCP computation for sequence collections with applications

(2019) Lavinia Egidi et al.   Algorithms for Molecular Biology

SNPs detection by eBWT positional clustering

(2019) Nicola Prezza et al.   Algorithms for Molecular Biology

The Alternating BWT: An algorithmic perspective

(2019) Raffaele Giancarlo et al.   THEORETICAL COMPUTER SCIENCE

Measuring the clustering effect of BWT via RLE

(2017) Sabrina Mantaci et al.   THEORETICAL COMPUTER SCIENCE

Wheeler graphs: A framework for BWT-based data structures

(2017) Travis Gagie et al.   THEORETICAL COMPUTER SCIENCE

Accurate self-correction of errors in long reads using de Bruijn graphs

(2016) Leena Salmela et al.   BIOINFORMATICS

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

(2016) Dirk D. Dolle et al.   GENOME RESEARCH

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes

(2016) Paola Bonizzoni et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Ultrafast SNP analysis using the Burrows–Wheeler transform of short-read data

(2015) Kouichi Kimura et al.   BIOINFORMATICS

HapCol: accurate and memory-efficient haplotype assembly from long reads

(2015) Yuri Pirola et al.   BIOINFORMATICS

Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data

(2015) Kouichi Kimura et al.   BMC BIOINFORMATICS

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

(2015) Murray Patterson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Indexing Arbitrary-Length k-Mers in Sequencing Reads

(2015) Tomasz Kowalski et al.   PLoS One

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

Reference-free SNP detection: dealing with the data deluge

(2014) Richard M Leggett et al.   BMC GENOMICS

Reference-free detection of isolated SNPs

(2014) Raluca Uricaru et al.   NUCLEIC ACIDS RESEARCH

Adaptive reference-free compression of sequence quality scores

(2013) L. Janin et al.   BIOINFORMATICS

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences

(2013) Christina Ander et al.   BMC BIOINFORMATICS

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs

(2013) Richard M. Leggett et al.   PLoS One

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

(2012) A. J. Cox et al.   BIOINFORMATICS

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

Lightweight algorithms for constructing and inverting the BWT of string collections

(2012) Markus J. Bauer et al.   THEORETICAL COMPUTER SCIENCE

Querying large read collections in main memory: a versatile data structure

(2011) Nicolas Philippe et al.   BMC BIOINFORMATICS

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Balancing and clustering of words in the Burrows–Wheeler transform

(2010) Antonio Restivo et al.   THEORETICAL COMPUTER SCIENCE

The Burrows–Wheeler similarity distribution between biological sequences based on Burrows–Wheeler transform

(2009) Lianping Yang et al.   JOURNAL OF THEORETICAL BIOLOGY

Distance measures for biological sequences: Some recent approaches

(2007) Sabrina Mantaci et al.   INTERNATIONAL JOURNAL OF APPROXIMATE REASONING