Author: Tobias Marschall

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Preprints

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

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  • In genomics: 34 out of 6,221
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  • Site-wide: 1,009 out of 100,306
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  • Site-wide: None out of 100,306

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

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  • In genomics: 72 out of 6,221
• Year to date:
  • Site-wide: 21,146 out of 100,306
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Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit

• Downloaded 7,908 times
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  • Site-wide: 391 out of 100,306
  • In bioinformatics: 50 out of 9,217
• Year to date:
  • Site-wide: 538 out of 100,306
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  • Site-wide: None out of 100,306

WhatsHap: fast and accurate read-based phasing

• Downloaded 6,998 times
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  • In bioinformatics: 64 out of 9,217
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  • Site-wide: 605 out of 100,306

A robust benchmark for germline structural variant detection

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  • In genomics: 164 out of 6,221
• Year to date:
  • Site-wide: 765 out of 100,306
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  • Site-wide: None out of 100,306

Computational Pan-Genomics: Status, Promises and Challenges

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  • In genomics: 213 out of 6,221
• Year to date:
  • Site-wide: 17,371 out of 100,306
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  • Site-wide: None out of 100,306

Accurate chromosome-scale haplotype-resolved assembly of human genomes

• Downloaded 2,906 times
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  • Site-wide: 2,117 out of 100,306
  • In bioinformatics: 373 out of 9,217
• Year to date:
  • Site-wide: 1,459 out of 100,306
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  • Site-wide: None out of 100,306

Haplotype-aware genotyping from noisy long reads

• Downloaded 2,714 times
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  • In bioinformatics: 420 out of 9,217
• Year to date:
  • Site-wide: 21,970 out of 100,306
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  • Site-wide: 7,658 out of 100,306

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

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  • In genomics: 532 out of 6,221
• Year to date:
  • Site-wide: 63,277 out of 100,306
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A fully phased accurate assembly of an individual human genome

• Downloaded 1,932 times
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  • In bioinformatics: 748 out of 9,217
• Year to date:
  • Site-wide: 2,190 out of 100,306
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  • Site-wide: None out of 100,306

GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment

• Downloaded 1,415 times
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  • In bioinformatics: 1,226 out of 9,217
• Year to date:
  • Site-wide: 4,592 out of 100,306
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  • Site-wide: None out of 100,306

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

• Downloaded 1,206 times
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  • Site-wide: 9,206 out of 100,306
  • In genetics: 632 out of 4,997
• Year to date:
  • Site-wide: 68,442 out of 100,306
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  • Site-wide: None out of 100,306

Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries

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  • Site-wide: 10,811 out of 100,306
  • In bioinformatics: 1,769 out of 9,217
• Year to date:
  • Site-wide: 81,411 out of 100,306
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  • Site-wide: None out of 100,306

Haplotype Threading: Accurate Polyploid Phasing from Long Reads

• Downloaded 953 times
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  • In bioinformatics: 2,117 out of 9,217
• Year to date:
  • Site-wide: 2,239 out of 100,306
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  • Site-wide: None out of 100,306

Bit-parallel sequence-to-graph alignment

• Downloaded 940 times
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  • Site-wide: 13,769 out of 100,306
  • In bioinformatics: 2,156 out of 9,217
• Year to date:
  • Site-wide: 57,731 out of 100,306
• Since beginning of last month:
  • Site-wide: 8,907 out of 100,306

Dense And Accurate Whole-Chromosome Haplotyping Of Individual Genomes

• Downloaded 931 times
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  • Site-wide: 14,012 out of 100,306
  • In bioinformatics: 2,187 out of 9,217
• Year to date:
  • Site-wide: 82,936 out of 100,306
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  • Site-wide: None out of 100,306

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

• Downloaded 920 times
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  • Site-wide: 14,270 out of 100,306
  • In bioinformatics: 2,223 out of 9,217
• Year to date:
  • Site-wide: 52,012 out of 100,306
• Since beginning of last month:
  • Site-wide: 10,776 out of 100,306

Read-Based Phasing of Related Individuals

• Downloaded 825 times
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  • Site-wide: 16,887 out of 100,306
  • In bioinformatics: 2,561 out of 9,217
• Year to date:
  • Site-wide: 94,248 out of 100,306
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  • Site-wide: None out of 100,306

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

• Downloaded 757 times
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  • In genomics: 2,299 out of 6,221
• Year to date:
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AERON: Transcript quantification and gene-fusion detection using long reads

• Downloaded 686 times
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  • Site-wide: 22,287 out of 100,306
  • In bioinformatics: 3,178 out of 9,217
• Year to date:
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  • Site-wide: 5,218 out of 100,306

Enhancing sensitivity and controlling false discovery rate in somatic indel discovery

• Downloaded 569 times
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  • Site-wide: 28,925 out of 100,306
  • In bioinformatics: 3,873 out of 9,217
• Year to date:
  • Site-wide: 32,760 out of 100,306
• Since beginning of last month:
  • Site-wide: 10,627 out of 100,306

Genotyping of Inversions and Tandem Duplications

• Downloaded 541 times
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  • In bioinformatics: 4,066 out of 9,217
• Year to date:
  • Site-wide: 93,081 out of 100,306
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  • Site-wide: None out of 100,306

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

• Downloaded 454 times
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  • Site-wide: 38,202 out of 100,306
  • In genomics: 3,601 out of 6,221
• Year to date:
  • Site-wide: 31,597 out of 100,306
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  • Site-wide: None out of 100,306

Selecting Reads for Haplotype Assembly

• Downloaded 451 times
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  • Site-wide: 38,520 out of 100,306
  • In bioinformatics: 4,774 out of 9,217
• Year to date:
  • Site-wide: 93,105 out of 100,306
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  • Site-wide: None out of 100,306

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

• Downloaded 450 times
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  • Site-wide: 38,701 out of 100,306
  • In bioinformatics: 4,790 out of 9,217
• Year to date:
  • Site-wide: 82,067 out of 100,306
• Since beginning of last month:
  • Site-wide: 15,793 out of 100,306

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

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  • Site-wide: 40,539 out of 100,306
  • In genomics: 3,747 out of 6,221
• Year to date:
  • Site-wide: 7,526 out of 100,306
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  • Site-wide: None out of 100,306

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

• Downloaded 311 times
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  • Site-wide: 55,976 out of 100,306
  • In bioinformatics: 6,255 out of 9,217
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  • Site-wide: 15,196 out of 100,306

MBG: Minimizer-based Sparse de Bruijn Graph Construction

• Downloaded 245 times
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  • Site-wide: 66,689 out of 100,306
  • In bioinformatics: 7,007 out of 9,217
• Year to date:
  • Site-wide: 17,553 out of 100,306
• Since beginning of last month:
  • Site-wide: 716 out of 100,306

A multi-platform reference for somatic structural variation detection

• Downloaded 46 times
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  • Site-wide: 95,947 out of 100,306
  • In genomics: 6,049 out of 6,221
• Year to date:
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• Since beginning of last month:
  • Site-wide: 6,015 out of 100,306