DIDA: Distributed Indexing Dispatched Alignment

Using cascading Bloom filters to improve the memory usage for de Brujin graphs

(2014) Kamil Salikhov et al.   Algorithms for Molecular Biology

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

(2014) Justin Chu et al.   BIOINFORMATICS

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data

(2013) Inanc Birol et al.   BIOINFORMATICS

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Lightweight Data Indexing and Compression in External Memory

(2011) Paolo Ferragina et al.   ALGORITHMICA

Efficient counting of k-mers in DNA sequences using a bloom filter

(2011) Páll Melsted et al.   BMC BIOINFORMATICS

Efficient de novo assembly of large genomes using compressed data structures

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

Classification of DNA sequences using Bloom filters

(2010) Henrik Stranneheim et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

mrsFAST: a cache-oblivious algorithm for short-read mapping

(2010) Faraz Hach et al.   NATURE METHODS

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

(2009) Yangho Chen et al.   BIOINFORMATICS

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Compressed indexing and local alignment of DNA

(2008) T. W. Lam et al.   BIOINFORMATICS

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH