Evidence map›Paper›PMID 33883006›Full record

ArticleGenome biology2021

AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data.

Kyle Fletcher, Lin Zhang, Juliana Gil, Rongkui Han, Keri Cavanaugh, Richard Michelmore

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Kyle FletcherThe Genome Center, University of California, Davis, USA.
Lin ZhangThe Genome Center, University of California, Davis, USA.
Juliana GilThe Genome Center, University of California, Davis, USA.
Rongkui HanThe Genome Center, University of California, Davis, USA.
Keri CavanaughThe Genome Center, University of California, Davis, USA.
Richard MichelmoreThe Genome Center, University of California, Davis, USA. rwmichelmore@ucdavis.edu.

Funding

Acquisition of Covaris E220 and Sciclone G3 systems for high throughput sequencinS10OD010786 · OD · UNIVERSITY OF CALIFORNIA AT DAVIS · PI COMAI, LUCA · 2012 to 2012
$311k
NIH HHS S10 OD010786
6 · The paper itself

Abstract

Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.

Indexed as

Genetic LinkageAmplified Fragment Length Polymorphism AnalysisArabidopsisChromosome MappingComputational BiologyExome SequencingGenome, PlantGenomicsArabidopsisBremiaGBSGenetic mapGenotype-by-sequencingK-merLettuceOomycete

Identifiers

PMID33883006
PMCPMC8061198

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.