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Author: Ben Langmead

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  • All-time downloads: 50,681 (rank: 677 out of 361,769)
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    • bioinformatics: 40,495 (rank: 62 out of 31,271)
    • genomics: 9,472 (rank: 1,457 (tie) out of 39,128)
    • neuroscience: 714 (rank: 21,167 (tie) out of 60,770)

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Preprints

Flexible analysis of transcriptome assemblies with Ballgown

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recount: A large-scale resource of analysis-ready RNA-seq expression data

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Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

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HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts

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Dashing: Fast and Accurate Genomic Distances with HyperLogLog

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Human splicing diversity across the Sequence Read Archive

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Improved metagenomic analysis with Kraken 2

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Flexible expressed region analysis for RNA-seq with derfinder

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Polyester: simulating RNA-seq datasets with differential transcript expression

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Scaling read aligners to hundreds of threads on general-purpose processors

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Analyzing whole genome bisulfite sequencing data from highly divergent genotypes

genomics more details view paper
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    • In genomics: 815 out of 5,423
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Lighter: fast and memory-efficient error correction without counting

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Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

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Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce

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    • Site-wide: 35,558 out of 84,017

FORGe: prioritizing variants for graph genomes

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    • In bioinformatics: 1,822 out of 8,053
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    • Site-wide: 65,168 out of 84,017

Samovar: Single-sample mosaic SNV calling with linked reads

genomics more details view paper
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Reducing reference bias using multiple population reference genomes

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Snaptron: querying and visualizing splicing across tens of thousands of RNA-seq samples

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A tandem simulation framework for predicting mapping quality

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Recounting the FANTOM Cage Associated Transcriptome

genomics more details view paper
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Boiler: Lossy compression of RNA-seq alignments using coverage vectors

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ASCOT identifies key regulators of neuronal subtype-specific splicing

neuroscience more details view paper
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    • Site-wide: 52,015 out of 84,017

Vargas: heuristic-free alignment for assessing linear and graph read aligners

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Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

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Prefix-Free Parsing for Building Big BWTs

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