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Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 57,812 bioRxiv papers from 266,109 authors.

Author: Adam M Phillippy

  • ORCiD: http://orcid.org/0000-0003-2983-8934
  • Most recently observed institution: Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health

Rankings

  • All-time downloads: 86,633 (rank: 71 out of 266,142)
  • Categories:
    • bioinformatics: 48,390 (rank: 40 out of 23,193)
    • genetics: 338 (rank: 17,244 (tie) out of 25,354)
    • genomics: 36,880 (rank: 132 out of 30,376)
    • microbiology: 1,025 (rank: 2,915 (tie) out of 26,512)

Downloads per author, site-wide

Preprints

Chromosome-length haplotigs for yak and cattle from trio binning assembly of an F1 hybrid

bioinformatics more details view paper

No bioRxiv download data for this paper yet.

Nanopore sequencing and assembly of a human genome with ultra-long reads

genomics more details view paper
  • Downloaded 12,838 times
  • Download rankings, all-time:
    • Site-wide: 62 out of 57,822
    • In genomics: 17 out of 4,058
  • Year to date:
    • Site-wide: 3,736 out of 57,822
  • Since beginning of last month:
    • Site-wide: 6,710 out of 57,822

Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing

bioinformatics more details view paper
  • Downloaded 10,644 times
  • Download rankings, all-time:
    • Site-wide: 89 out of 57,822
    • In bioinformatics: 15 out of 5,897
  • Year to date:
    • Site-wide: 3,761 out of 57,822
  • Since beginning of last month:
    • Site-wide: 3,100 out of 57,822

Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

genomics more details view paper
  • Downloaded 8,855 times
  • Download rankings, all-time:
    • Site-wide: 129 out of 57,822
    • In genomics: 42 out of 4,058
  • Year to date:
    • Site-wide: 16 out of 57,822
  • Since beginning of last month:
    • Site-wide: 54 out of 57,822

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

bioinformatics more details view paper
  • Downloaded 7,484 times
  • Download rankings, all-time:
    • Site-wide: 169 out of 57,822
    • In bioinformatics: 29 out of 5,897
  • Year to date:
    • Site-wide: 5,019 out of 57,822
  • Since beginning of last month:
    • Site-wide: 11,188 out of 57,822

Mash: fast genome and metagenome distance estimation using MinHash

bioinformatics more details view paper
  • Downloaded 6,295 times
  • Download rankings, all-time:
    • Site-wide: 240 out of 57,822
    • In bioinformatics: 44 out of 5,897
  • Year to date:
    • Site-wide: 15,924 out of 57,822
  • Since beginning of last month:
    • Site-wide: 11,718 out of 57,822

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

bioinformatics more details view paper
  • Downloaded 5,658 times
  • Download rankings, all-time:
    • Site-wide: 302 out of 57,822
    • In bioinformatics: 56 out of 5,897
  • Year to date:
    • Site-wide: 255 out of 57,822
  • Since beginning of last month:
    • Site-wide: 689 out of 57,822

A fast approximate algorithm for mapping long reads to large reference databases

bioinformatics more details view paper
  • Downloaded 3,626 times
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    • Site-wide: 700 out of 57,822
    • In bioinformatics: 133 out of 5,897
  • Year to date:
    • Site-wide: 4,308 out of 57,822
  • Since beginning of last month:
    • Site-wide: 3,413 out of 57,822

Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

genomics more details view paper
  • Downloaded 3,041 times
  • Download rankings, all-time:
    • Site-wide: 975 out of 57,822
    • In genomics: 242 out of 4,058
  • Year to date:
    • Site-wide: 22,178 out of 57,822
  • Since beginning of last month:
    • Site-wide: 17,645 out of 57,822

Improved Aedes aegypti mosquito reference genome assembly enables biological discovery and vector control

genomics more details view paper
  • Downloaded 2,977 times
  • Download rankings, all-time:
    • Site-wide: 1,001 out of 57,822
    • In genomics: 248 out of 4,058
  • Year to date:
    • Site-wide: 3,982 out of 57,822
  • Since beginning of last month:
    • Site-wide: 4,109 out of 57,822

Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes

bioinformatics more details view paper
  • Downloaded 2,824 times
  • Download rankings, all-time:
    • Site-wide: 1,116 out of 57,822
    • In bioinformatics: 231 out of 5,897
  • Year to date:
    • Site-wide: 16,145 out of 57,822
  • Since beginning of last month:
    • Site-wide: 23,611 out of 57,822

High-throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries

bioinformatics more details view paper
  • Downloaded 2,780 times
  • Download rankings, all-time:
    • Site-wide: 1,154 out of 57,822
    • In bioinformatics: 241 out of 5,897
  • Year to date:
    • Site-wide: 7,114 out of 57,822
  • Since beginning of last month:
    • Site-wide: 15,130 out of 57,822

Automated ensemble assembly and validation of microbial genomes

bioinformatics more details view paper
  • Downloaded 1,901 times
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    • Site-wide: 2,254 out of 57,822
    • In bioinformatics: 465 out of 5,897
  • Year to date:
    • Site-wide: 54,185 out of 57,822
  • Since beginning of last month:
    • Site-wide: 49,731 out of 57,822

Long-read, whole genome shotgun sequence data for five model organisms

genomics more details view paper
  • Downloaded 1,796 times
  • Download rankings, all-time:
    • Site-wide: 2,462 out of 57,822
    • In genomics: 507 out of 4,058
  • Year to date:
    • Site-wide: 28,547 out of 57,822
  • Since beginning of last month:
    • Site-wide: 29,686 out of 57,822

A robust benchmark for germline structural variant detection

genomics more details view paper
  • Downloaded 1,791 times
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    • Site-wide: 2,484 out of 57,822
    • In genomics: 512 out of 4,058
  • Year to date:
    • Site-wide: 348 out of 57,822
  • Since beginning of last month:
    • Site-wide: 178 out of 57,822

A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps

bioinformatics more details view paper
  • Downloaded 1,761 times
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    • Site-wide: 2,561 out of 57,822
    • In bioinformatics: 525 out of 5,897
  • Year to date:
    • Site-wide: 8,101 out of 57,822
  • Since beginning of last month:
    • Site-wide: 11,504 out of 57,822

De Novo assembly of the goldfish (Carassius auratus) genome and the evolution of genes after whole genome duplication

genomics more details view paper
  • Downloaded 1,683 times
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    • Site-wide: 2,775 out of 57,822
    • In genomics: 563 out of 4,058
  • Year to date:
    • Site-wide: 3,078 out of 57,822
  • Since beginning of last month:
    • Site-wide: 5,668 out of 57,822

RefSeq database growth influences the accuracy of k-mer-based species identification

bioinformatics more details view paper
  • Downloaded 1,282 times
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    • Site-wide: 4,339 out of 57,822
    • In bioinformatics: 866 out of 5,897
  • Year to date:
    • Site-wide: 20,412 out of 57,822
  • Since beginning of last month:
    • Site-wide: 12,893 out of 57,822

MetaMaps - Strain-level metagenomic assignment and compositional estimation for long reads

bioinformatics more details view paper
  • Downloaded 1,248 times
  • Download rankings, all-time:
    • Site-wide: 4,531 out of 57,822
    • In bioinformatics: 901 out of 5,897
  • Year to date:
    • Site-wide: 7,243 out of 57,822
  • Since beginning of last month:
    • Site-wide: 7,664 out of 57,822

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

genomics more details view paper
  • Downloaded 1,119 times
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    • Site-wide: 5,405 out of 57,822
    • In genomics: 924 out of 4,058
  • Year to date:
    • Site-wide: 30,507 out of 57,822
  • Since beginning of last month:
    • Site-wide: 30,782 out of 57,822

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

microbiology more details view paper
  • Downloaded 1,025 times
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    • Site-wide: 6,284 out of 57,822
    • In microbiology: 245 out of 4,604
  • Year to date:
    • Site-wide: 2,386 out of 57,822
  • Since beginning of last month:
    • Site-wide: 4,221 out of 57,822

Mash Screen: High-throughput sequence containment estimation for genome discovery

bioinformatics more details view paper
  • Downloaded 984 times
  • Download rankings, all-time:
    • Site-wide: 6,696 out of 57,822
    • In bioinformatics: 1,220 out of 5,897
  • Year to date:
    • Site-wide: 1,146 out of 57,822
  • Since beginning of last month:
    • Site-wide: 3,216 out of 57,822

Telomere-to-telomere assembly of a complete human X chromosome

bioinformatics more details view paper
  • Downloaded 925 times
  • Download rankings, all-time:
    • Site-wide: 7,390 out of 57,822
    • In bioinformatics: 1,331 out of 5,897
  • Year to date:
    • Site-wide: 1,253 out of 57,822
  • Since beginning of last month:
    • Site-wide: 87 out of 57,822

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation

genomics more details view paper
  • Downloaded 730 times
  • Download rankings, all-time:
    • Site-wide: 10,578 out of 57,822
    • In genomics: 1,528 out of 4,058
  • Year to date:
    • Site-wide: 40,261 out of 57,822
  • Since beginning of last month:
    • Site-wide: 35,952 out of 57,822

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

genomics more details view paper
  • Downloaded 659 times
  • Download rankings, all-time:
    • Site-wide: 12,244 out of 57,822
    • In genomics: 1,697 out of 4,058
  • Year to date:
    • Site-wide: 6,737 out of 57,822
  • Since beginning of last month:
    • Site-wide: 12,518 out of 57,822

HLA*PRG:LA - HLA typing from linearly projected graph alignments

bioinformatics more details view paper
  • Downloaded 542 times
  • Download rankings, all-time:
    • Site-wide: 15,913 out of 57,822
    • In bioinformatics: 2,497 out of 5,897
  • Year to date:
    • Site-wide: 11,988 out of 57,822
  • Since beginning of last month:
    • Site-wide: 18,273 out of 57,822

The whale shark genome reveals patterns of vertebrate gene family evolution

genomics more details view paper
  • Downloaded 509 times
  • Download rankings, all-time:
    • Site-wide: 17,242 out of 57,822
    • In genomics: 2,113 out of 4,058
  • Year to date:
    • Site-wide: 3,566 out of 57,822
  • Since beginning of last month:
    • Site-wide: 745 out of 57,822

An improved pig reference genome sequence to enable pig genetics and genomics research

genomics more details view paper
  • Downloaded 496 times
  • Download rankings, all-time:
    • Site-wide: 17,790 out of 57,822
    • In genomics: 2,146 out of 4,058
  • Year to date:
    • Site-wide: 3,746 out of 57,822
  • Since beginning of last month:
    • Site-wide: 1,735 out of 57,822

A chromosome-scale assembly of the major African malaria vector Anopheles funestus

bioinformatics more details view paper
  • Downloaded 436 times
  • Download rankings, all-time:
    • Site-wide: 20,701 out of 57,822
    • In bioinformatics: 3,021 out of 5,897
  • Year to date:
    • Site-wide: 9,075 out of 57,822
  • Since beginning of last month:
    • Site-wide: 22,775 out of 57,822

The evolution of the natural killer complex; a comparison between mammals using new high-quality genome assemblies and targeted annotation

genetics more details view paper
  • Downloaded 338 times
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    • Site-wide: 26,952 out of 57,822
    • In genetics: 1,756 out of 3,318
  • Year to date:
    • Site-wide: 49,466 out of 57,822
  • Since beginning of last month:
    • Site-wide: 49,427 out of 57,822

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

genomics more details view paper
  • Downloaded 234 times
  • Download rankings, all-time:
    • Site-wide: 36,460 out of 57,822
    • In genomics: 3,263 out of 4,058
  • Year to date:
    • Site-wide: 12,322 out of 57,822
  • Since beginning of last month:
    • Site-wide: 1,036 out of 57,822

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

genomics more details view paper
  • Downloaded 152 times
  • Download rankings, all-time:
    • Site-wide: 46,210 out of 57,822
    • In genomics: 3,663 out of 4,058
  • Year to date:
    • Site-wide: 21,473 out of 57,822
  • Since beginning of last month:
    • Site-wide: 4,485 out of 57,822

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