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Author: Steven L. Salzberg

Rankings

  • All-time downloads: 65,200 (rank: 501 out of 360,279)
  • Categories:
    • bioinformatics: 44,547 (rank: 57 out of 31,168)
    • genomics: 20,286 (rank: 413 out of 39,022)
    • microbiology: 367 (rank: 19,782 (tie) out of 39,486)

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Preprints

Flexible analysis of transcriptome assemblies with Ballgown

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Thousands of large-scale RNA sequencing experiments yield a comprehensive new human gene list and reveal extensive transcriptional noise

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Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the mega-reads algorithm

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The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

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Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification

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Centrifuge: rapid and sensitive classification of metagenomic sequences

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HISAT: Hierarchical Indexing for Spliced Alignment of Transcripts

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KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts

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Bracken: Estimating species abundance in metagenomics data

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Removing Contaminants from Metagenomic Databases

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HISAT-genotype: Next Generation Genomic Analysis Platform on a Personal Computer

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Next-generation sequencing in neuropathological diagnosis of infections of the nervous system

genomics more details view paper
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Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

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Transcriptome assembly from long-read RNA-seq alignments with StringTie2

genomics more details view paper
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The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order

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

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16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model

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The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies

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The giant sequoia genome and proliferation of disease resistance genes

genomics more details view paper
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High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome

genomics more details view paper
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Ultrafast and accurate 16S microbial community analysis using Kraken 2

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Chromosome-scale assembly of the bread wheat genome, Triticum aestivum, reveals over 5700 new genes

genomics more details view paper
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First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans)

microbiology more details view paper
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Assembly and Annotation of an Ashkenazi Human Reference Genome

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SkewIT: Skew Index Test for detecting mis-assembled bacterial genomes

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