Computing the multi-string BWT and LCP array in external memory

External memory BWT and LCP computation for sequence collections with applications

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

Inducing enhanced suffix arrays for string collections

(2017) Felipe A. Louza et al.   THEORETICAL COMPUTER SCIENCE

Wheeler graphs: A framework for BWT-based data structures

(2017) Travis Gagie et al.   THEORETICAL COMPUTER SCIENCE

An External-Memory Algorithm for String Graph Construction

(2016) Paola Bonizzoni et al.   ALGORITHMICA

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly

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

Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)

(2014) R. Durbin   BIOINFORMATICS

Fast construction of FM-index for long sequence reads

(2014) H. Li   BIOINFORMATICS

Merging of multi-string BWTs with applications

(2014) J. Holt et al.   BIOINFORMATICS

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

Lightweight algorithms for constructing and inverting the BWT of string collections

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

Lightweight Data Indexing and Compression in External Memory

(2011) Paolo Ferragina et al.   ALGORITHMICA

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Efficient construction of an assembly string graph using the FM-index

(2010) J. T. Simpson et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Compressing and indexing labeled trees, with applications

(2009) Paolo Ferragina et al.   JOURNAL OF THE ACM

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY