• Publications
  • Influence
Fast gapped-read alignment with Bowtie 2
As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach isExpand
  • 19,946
  • 2552
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25Expand
  • 15,841
  • 2180
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotationsExpand
  • 9,723
  • 1377
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. In this paper, we describe TopHat2, which incorporates many significant enhancements to TopHat. TopHat2 can align reads ofExpand
  • 8,260
  • 1131
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data fromExpand
  • 7,968
  • 1079
HISAT: a fast spliced aligner with low memory requirements
HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on theExpand
  • 4,493
  • 595
Versatile and open software for comparing large genomes
The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewingExpand
  • 3,655
  • 449
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
Methods used to sequence the transcriptome often produce more than 200 million short sequences. We introduce StringTie, a computational method that applies a network flow algorithm originallyExpand
  • 1,901
  • 301
Programs for Machine Learning
Algorithms for constructing decision trees are among the most well known and widely used of all machine learning methods. Among decision tree algorithms, J. Ross Quinlan's ID3 and its successor,Expand
  • 5,092
  • 286
Kraken: ultrafast metagenomic sequence classification using exact alignments
Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationallyExpand
  • 1,826
  • 266