• 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
  • 19,944
  • 2551
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
  • 15,840
  • 2180
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
Aligning Short Sequencing Reads with Bowtie
  • B. Langmead
  • Medicine, Biology
  • Current protocols in bioinformatics
  • 1 December 2010
This unit shows how to use the Bowtie package to align short sequencing reads, such as those output by second‐generation sequencing instruments. It also includes protocols for building a genome indexExpand
  • 699
  • 101
Ballgown bridges the gap between transcriptome assembly and expression analysis
Analysis of raw reads from RNA sequencing (RNA-seq) makes it possible to reconstruct complete gene structures, including multiple splice variants, without relying on previously establishedExpand
  • 250
  • 46
Searching for SNPs with cloud computing
As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines theExpand
  • 482
  • 35
Lighter: fast and memory-efficient sequencing error correction without counting
Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input k-mers and theExpand
  • 156
  • 23
Improved metagenomic analysis with Kraken 2
Although Kraken’s k-mer-based approach provides fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves uponExpand
  • 101
  • 21
Polyester: simulating RNA-seq datasets with differential transcript expression
MOTIVATION Statistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differentialExpand
  • 149
  • 17
Cloud-scale RNA-sequencing differential expression analysis with Myrna
As sequencing throughput approaches dozens of gigabases per day, there is a growing need for efficient software for analysis of transcriptome sequencing (RNA-Seq) data. Myrna is a cloud-computingExpand
  • 301
  • 15