Author: Tobias Marschall

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Preprints

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

• Downloaded 12,841 times
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  • Site-wide: 536
  • In genomics: 37
• Year to date:
  • Site-wide: 3,547
• Since beginning of last month:
  • Site-wide: 3,291

Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit

• Downloaded 8,533 times
• Download rankings, all-time:
  • Site-wide: 930
  • In bioinformatics: 54
• Year to date:
  • Site-wide: 6,914
• Since beginning of last month:
  • Site-wide: 9,689

Multi-platform discovery of haplotype-resolved structural variation in human genomes

• Downloaded 8,336 times
• Download rankings, all-time:
  • Site-wide: 953
  • In genomics: 84
• Year to date:
  • Site-wide: 46,918
• Since beginning of last month:
  • Site-wide: None

WhatsHap: fast and accurate read-based phasing

• Downloaded 7,842 times
• Download rankings, all-time:
  • Site-wide: 1,028
  • In bioinformatics: 62
• Year to date:
  • Site-wide: 1,865
• Since beginning of last month:
  • Site-wide: 2,007

A robust benchmark for germline structural variant detection

• Downloaded 5,670 times
• Download rankings, all-time:
  • Site-wide: 1,582
  • In genomics: 150
• Year to date:
  • Site-wide: 4,767
• Since beginning of last month:
  • Site-wide: 4,660

Computational Pan-Genomics: Status, Promises and Challenges

• Downloaded 4,605 times
• Download rankings, all-time:
  • Site-wide: 2,095
  • In genomics: 227
• Year to date:
  • Site-wide: 18,732
• Since beginning of last month:
  • Site-wide: 30,021

Accurate chromosome-scale haplotype-resolved assembly of human genomes

• Downloaded 3,780 times
• Download rankings, all-time:
  • Site-wide: 2,771
  • In bioinformatics: 269
• Year to date:
  • Site-wide: 5,017
• Since beginning of last month:
  • Site-wide: 8,132

Haplotype-aware genotyping from noisy long reads

• Downloaded 2,786 times
• Download rankings, all-time:
  • Site-wide: 4,287
  • In bioinformatics: 465
• Year to date:
  • Site-wide: 44,750
• Since beginning of last month:
  • Site-wide: 44,893

Mapping And Phasing Of Structural Variation In Patient Genomes Using Nanopore Sequencing

• Downloaded 2,471 times
• Download rankings, all-time:
  • Site-wide: 5,138
  • In genomics: 605
• Year to date:
  • Site-wide: 112,794
• Since beginning of last month:
  • Site-wide: None

A fully phased accurate assembly of an individual human genome

• Downloaded 2,430 times
• Download rankings, all-time:
  • Site-wide: 5,270
  • In bioinformatics: 600
• Year to date:
  • Site-wide: 15,639
• Since beginning of last month:
  • Site-wide: 24,135

GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment

• Downloaded 1,730 times
• Download rankings, all-time:
  • Site-wide: 8,697
  • In bioinformatics: 1,068
• Year to date:
  • Site-wide: 26,856
• Since beginning of last month:
  • Site-wide: 24,767

Benchmarking challenging small variants with linked and long reads

• Downloaded 1,384 times
• Download rankings, all-time:
  • Site-wide: 12,132
  • In genomics: 1,340
• Year to date:
  • Site-wide: 3,201
• Since beginning of last month:
  • Site-wide: 2,687

A high-quality reference panel reveals the complexity and distribution of structural genome changes in a human population

• Downloaded 1,275 times
• Download rankings, all-time:
  • Site-wide: 13,707
  • In genetics: 697
• Year to date:
  • Site-wide: 64,441
• Since beginning of last month:
  • Site-wide: 64,293

Haplotype Threading: Accurate Polyploid Phasing from Long Reads

• Downloaded 1,254 times
• Download rankings, all-time:
  • Site-wide: 14,064
  • In bioinformatics: 1,736
• Year to date:
  • Site-wide: 29,595
• Since beginning of last month:
  • Site-wide: 41,168

Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries

• Downloaded 1,135 times
• Download rankings, all-time:
  • Site-wide: 16,367
  • In bioinformatics: 2,010
• Year to date:
  • Site-wide: 94,022
• Since beginning of last month:
  • Site-wide: 83,642

Bit-parallel sequence-to-graph alignment

• Downloaded 983 times
• Download rankings, all-time:
  • Site-wide: 20,217
  • In bioinformatics: 2,440
• Year to date:
  • Site-wide: 73,654
• Since beginning of last month:
  • Site-wide: 38,347

Dense And Accurate Whole-Chromosome Haplotyping Of Individual Genomes

• Downloaded 980 times
• Download rankings, all-time:
  • Site-wide: 20,313
  • In bioinformatics: 2,445
• Year to date:
  • Site-wide: 65,628
• Since beginning of last month:
  • Site-wide: 83,846

Aligning sequences to general graphs in O(V + mE) time

• Downloaded 963 times
• Download rankings, all-time:
  • Site-wide: 20,807
  • In bioinformatics: 2,504
• Year to date:
  • Site-wide: 58,297
• Since beginning of last month:
  • Site-wide: 50,507

Pangenome-based genome inference

• Downloaded 934 times
• Download rankings, all-time:
  • Site-wide: 21,767
  • In bioinformatics: 2,608
• Year to date:
  • Site-wide: 5,529
• Since beginning of last month:
  • Site-wide: 5,549

A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex

• Downloaded 867 times
• Download rankings, all-time:
  • Site-wide: 24,240
  • In genomics: 2,347
• Year to date:
  • Site-wide: 53,722
• Since beginning of last month:
  • Site-wide: 39,132

Read-Based Phasing of Related Individuals

• Downloaded 846 times
• Download rankings, all-time:
  • Site-wide: 25,093
  • In bioinformatics: 2,979
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: None

AERON: Transcript quantification and gene-fusion detection using long reads

• Downloaded 831 times
• Download rankings, all-time:
  • Site-wide: 25,727
  • In bioinformatics: 3,039
• Year to date:
  • Site-wide: 22,539
• Since beginning of last month:
  • Site-wide: 26,968

Expectations and blind spots for structural variation detection from short-read alignment and long-read assembly

• Downloaded 727 times
• Download rankings, all-time:
  • Site-wide: 31,001
  • In genomics: 2,812
• Year to date:
  • Site-wide: 14,360
• Since beginning of last month:
  • Site-wide: 16,775

Enhancing sensitivity and controlling false discovery rate in somatic indel discovery

• Downloaded 608 times
• Download rankings, all-time:
  • Site-wide: 39,220
  • In bioinformatics: 4,313
• Year to date:
  • Site-wide: 80,334
• Since beginning of last month:
  • Site-wide: 62,618

Genotyping of Inversions and Tandem Duplications

• Downloaded 569 times
• Download rankings, all-time:
  • Site-wide: 42,629
  • In bioinformatics: 4,585
• Year to date:
  • Site-wide: 107,080
• Since beginning of last month:
  • Site-wide: 77,465

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

• Downloaded 505 times
• Download rankings, all-time:
  • Site-wide: 49,188
  • In genomics: 3,914
• Year to date:
  • Site-wide: 90,665
• Since beginning of last month:
  • Site-wide: 98,277

Selecting Reads for Haplotype Assembly

• Downloaded 481 times
• Download rankings, all-time:
  • Site-wide: 52,132
  • In bioinformatics: 5,374
• Year to date:
  • Site-wide: 121,285
• Since beginning of last month:
  • Site-wide: 102,975

Enhancing Sensitivity And Controlling False Discovery Rate In Somatic Indel Discovery Using A Latent Variable Model

• Downloaded 462 times
• Download rankings, all-time:
  • Site-wide: 54,457
  • In bioinformatics: 5,579
• Year to date:
  • Site-wide: 119,246
• Since beginning of last month:
  • Site-wide: 98,069

A multi-platform reference for somatic structural variation detection

• Downloaded 449 times
• Download rankings, all-time:
  • Site-wide: 56,166
  • In genomics: 4,267
• Year to date:
  • Site-wide: 10,325
• Since beginning of last month:
  • Site-wide: 17,236

MBG: Minimizer-based Sparse de Bruijn Graph Construction

• Downloaded 355 times
• Download rankings, all-time:
  • Site-wide: 70,498
  • In bioinformatics: 6,702
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: None

Fully-sensitive Seed Finding in Sequence Graphs Using a Hybrid Index

• Downloaded 331 times
• Download rankings, all-time:
  • Site-wide: 74,802
  • In bioinformatics: 6,983
• Year to date:
  • Site-wide: 106,610
• Since beginning of last month:
  • Site-wide: 74,611