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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 73,530 bioRxiv papers from 320,012 authors.

Author: Michael C. Schatz

Rankings

  • All-time downloads: 114,980 (rank: 82 out of 319,830)
  • Categories:
    • bioinformatics: 90,368 (rank: 1 out of 27,742)
    • genomics: 24,612 (rank: 263 out of 35,681)

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Preprints

iGenomics: Comprehensive DNA Sequence Analysis on your Smartphone

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Third-generation sequencing and the future of genomics

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  • Downloaded 29,653 times
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    • Site-wide: 16 out of 73,481
    • In bioinformatics: 2 out of 7,157
  • Year to date:
    • Site-wide: 317 out of 73,481
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    • Site-wide: 317 out of 73,481

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

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  • Downloaded 10,846 times
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    • Site-wide: 122 out of 73,481
    • In genomics: 31 out of 4,874
  • Year to date:
    • Site-wide: 496 out of 73,481
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    • Site-wide: 496 out of 73,481

Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome

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  • Downloaded 9,818 times
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    • In bioinformatics: 23 out of 7,157
  • Year to date:
    • Site-wide: 42,217 out of 73,481
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Phased Diploid Genome Assembly with Single Molecule Real-Time Sequencing

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  • Downloaded 6,537 times
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    • In bioinformatics: 50 out of 7,157
  • Year to date:
    • Site-wide: 13,070 out of 73,481
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Accurate detection of complex structural variations using single molecule sequencing

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  • Downloaded 5,430 times
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    • In bioinformatics: 79 out of 7,157
  • Year to date:
    • Site-wide: 9,964 out of 73,481
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Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

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  • Downloaded 3,415 times
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    • In bioinformatics: 201 out of 7,157
  • Year to date:
    • Site-wide: 8,751 out of 73,481
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A robust benchmark for germline structural variant detection

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  • Downloaded 3,362 times
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    • In genomics: 255 out of 4,874
  • Year to date:
    • Site-wide: 991 out of 73,481
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Accurate detection of de novo and transmitted INDELs within exome-capture data using micro-assembly

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  • Downloaded 2,913 times
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    • In bioinformatics: 275 out of 7,157
  • Year to date:
    • Site-wide: 51,697 out of 73,481
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Fast and accurate reference-guided scaffolding of draft genomes

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  • Downloaded 2,906 times
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    • In bioinformatics: 278 out of 7,157
  • Year to date:
    • Site-wide: 3,468 out of 73,481
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    • Site-wide: 3,468 out of 73,481

The next 20 years of genome research

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  • Downloaded 2,842 times
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    • In bioinformatics: 288 out of 7,157
  • Year to date:
    • Site-wide: 62,776 out of 73,481
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    • Site-wide: 62,776 out of 73,481

Ribbon: Visualizing complex genome alignments and structural variation

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  • Downloaded 2,797 times
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    • In bioinformatics: 297 out of 7,157
  • Year to date:
    • Site-wide: 7,561 out of 73,481
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    • Site-wide: 7,561 out of 73,481

SplitMEM: Graphical pan-genome analysis with suffix skips

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  • Downloaded 2,378 times
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    • In bioinformatics: 400 out of 7,157
  • Year to date:
    • Site-wide: 63,077 out of 73,481
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    • Site-wide: 63,077 out of 73,481

Reducing INDEL calling errors in whole-genome and exome sequencing data

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  • Downloaded 2,360 times
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    • In bioinformatics: 405 out of 7,157
  • Year to date:
    • Site-wide: 39,043 out of 73,481
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Interactive analysis and quality assessment of single-cell copy-number variations

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  • Downloaded 2,254 times
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    • In bioinformatics: 442 out of 7,157
  • Year to date:
    • Site-wide: 41,896 out of 73,481
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    • Site-wide: 41,896 out of 73,481

Addressing confounding artifacts in reconstruction of gene co-expression networks

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  • Downloaded 2,090 times
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    • In genomics: 515 out of 4,874
  • Year to date:
    • Site-wide: 39,693 out of 73,481
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    • Site-wide: 39,693 out of 73,481

Indel variant analysis of short-read sequencing data with Scalpel

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  • Downloaded 2,089 times
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    • In bioinformatics: 495 out of 7,157
  • Year to date:
    • Site-wide: 59,681 out of 73,481
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    • Site-wide: 59,681 out of 73,481

Metassembler: Merging and optimizing de novo genome assemblies

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  • Downloaded 1,738 times
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    • In bioinformatics: 677 out of 7,157
  • Year to date:
    • Site-wide: 45,569 out of 73,481
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    • Site-wide: 45,569 out of 73,481

GenomeScope: Fast reference-free genome profiling from short reads

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    • In bioinformatics: 801 out of 7,157
  • Year to date:
    • Site-wide: 53,929 out of 73,481
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    • Site-wide: 53,929 out of 73,481

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

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  • Downloaded 1,558 times
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    • In genomics: 744 out of 4,874
  • Year to date:
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    • Site-wide: 54,563 out of 73,481

Paragraph: A graph-based structural variant genotyper for short-read sequence data

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  • Downloaded 1,513 times
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    • Site-wide: 4,381 out of 73,481
    • In genomics: 785 out of 4,874
  • Year to date:
    • Site-wide: 6,422 out of 73,481
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    • Site-wide: 6,422 out of 73,481

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED

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  • Downloaded 1,468 times
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    • Site-wide: 4,603 out of 73,481
    • In genomics: 823 out of 4,874
  • Year to date:
    • Site-wide: 72 out of 73,481
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    • Site-wide: 72 out of 73,481

The DOE Systems Biology Knowledgebase (KBase)

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    • In bioinformatics: 898 out of 7,157
  • Year to date:
    • Site-wide: 40,460 out of 73,481
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    • Site-wide: 40,460 out of 73,481

Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing

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  • Downloaded 1,452 times
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    • Site-wide: 4,695 out of 73,481
    • In bioinformatics: 900 out of 7,157
  • Year to date:
    • Site-wide: 1,265 out of 73,481
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    • Site-wide: 1,265 out of 73,481

Scikit-ribo: Accurate estimation and robust modeling of translation dynamics at codon resolution

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    • Site-wide: 5,818 out of 73,481
    • In bioinformatics: 1,099 out of 7,157
  • Year to date:
    • Site-wide: 42,382 out of 73,481
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    • Site-wide: 42,382 out of 73,481

Assemblytics: a web analytics tool for the detection of assembly-based variants

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  • Downloaded 1,204 times
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    • Site-wide: 6,436 out of 73,481
    • In genomics: 1,057 out of 4,874
  • Year to date:
    • Site-wide: 34,985 out of 73,481
  • Since beginning of last month:
    • Site-wide: 34,985 out of 73,481

LRSim: a Linked Reads Simulator generating insights for better genome partitioning

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    • Site-wide: 6,746 out of 73,481
    • In bioinformatics: 1,237 out of 7,157
  • Year to date:
    • Site-wide: 68,642 out of 73,481
  • Since beginning of last month:
    • Site-wide: 68,642 out of 73,481

GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes

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  • Downloaded 1,128 times
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    • Site-wide: 7,145 out of 73,481
    • In bioinformatics: 1,289 out of 7,157
  • Year to date:
    • Site-wide: 3,140 out of 73,481
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    • Site-wide: 3,140 out of 73,481

Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants

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    • Site-wide: 7,913 out of 73,481
    • In bioinformatics: 1,383 out of 7,157
  • Year to date:
    • Site-wide: 34,242 out of 73,481
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    • Site-wide: 34,242 out of 73,481

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

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    • Site-wide: 7,925 out of 73,481
    • In bioinformatics: 1,384 out of 7,157
  • Year to date:
    • Site-wide: 68,560 out of 73,481
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    • Site-wide: 68,560 out of 73,481

Reference Quality Assembly of the 3.5 Gb genome of Capsicum annuum from a Single Linked-Read Library

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  • Downloaded 1,048 times
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    • In genomics: 1,269 out of 4,874
  • Year to date:
    • Site-wide: 48,243 out of 73,481
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    • Site-wide: 48,243 out of 73,481

SplitThreader: Exploration and analysis of rearrangements in cancer genomes

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    • Site-wide: 9,680 out of 73,481
    • In bioinformatics: 1,644 out of 7,157
  • Year to date:
    • Site-wide: 41,172 out of 73,481
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    • Site-wide: 41,172 out of 73,481

Samovar: Single-sample mosaic SNV calling with linked reads

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  • Downloaded 901 times
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    • Site-wide: 10,320 out of 73,481
    • In genomics: 1,521 out of 4,874
  • Year to date:
    • Site-wide: 18,760 out of 73,481
  • Since beginning of last month:
    • Site-wide: 18,760 out of 73,481

SVCollector: Optimized sample selection for validating and long-read resequencing of structural variants

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  • Downloaded 713 times
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    • Site-wide: 14,694 out of 73,481
    • In bioinformatics: 2,325 out of 7,157
  • Year to date:
    • Site-wide: 22,598 out of 73,481
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    • Site-wide: 22,598 out of 73,481

First near complete haplotype phased genome assembly of River buffalo (Bubalus bubalis)

genomics more details view paper
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    • In genomics: 2,171 out of 4,874
  • Year to date:
    • Site-wide: 5,182 out of 73,481
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    • Site-wide: 5,182 out of 73,481

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data

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  • Downloaded 550 times
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    • Site-wide: 21,243 out of 73,481
    • In bioinformatics: 3,075 out of 7,157
  • Year to date:
    • Site-wide: 71,194 out of 73,481
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    • Site-wide: 71,194 out of 73,481

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

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    • Site-wide: 34,645 out of 73,481
    • In bioinformatics: 4,334 out of 7,157
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    • Site-wide: 4,731 out of 73,481
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    • Site-wide: 4,731 out of 73,481

Sapling: Accelerating Suffix Array Queries with Learned Data Models

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    • Site-wide: 39,554 out of 73,481
    • In bioinformatics: 4,771 out of 7,157
  • Year to date:
    • Site-wide: 774 out of 73,481
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    • Site-wide: 774 out of 73,481

Recovering rearranged cancer chromosomes from karyotype graphs

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    • In bioinformatics: 6,069 out of 7,157
  • Year to date:
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    • Site-wide: 43,979 out of 73,481

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