ArticleGenome biology2018
FORGe: prioritizing variants for graph genomes.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
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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.
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.
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Who cites it
51 citing papers in PubMed.
- Movi 2: fast and space-efficient queries on pangenomes.Bioinformatics (Oxford, England) · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Minimizing reference bias with an imputed personalized reference.Genome research · 2026Article
- Pangenome-based genome inference using integer programming.Genome research · 2025Article
- Movi 2: Fast and Space-Efficient Queries on Pangenomes.bioRxiv : the preprint server for biology · 2025Article
- Blended Length Genome Sequencing (blend-seq): Combining Short Reads with Low-Coverage Long Reads to Maximize Variant Discovery.bioRxiv : the preprint server for biology · 2025Article
- Accurate short-read alignment throughGenome research · 2025Article
- Review
- Gastric cancer genomics study using reference human pangenomes.Life science alliance · 2025Article
- Personalized pangenome references.Nature methods · 2024Article
- Integer programming framework for pangenome-based genome inference.bioRxiv : the preprint server for biology · 2024Article
- When less is more: sketching with minimizers in genomics.Genome biology · 2024Review
- Haplotype-aware sequence alignment to pangenome graphs.Genome research · 2024Article
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- Measuring, visualizing, and diagnosing reference bias with biastools.Genome biology · 2024Article
- Measuring, visualizing and diagnosing reference bias with biastools.bioRxiv : the preprint server for biology · 2024Article
- A hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.PloS one · 2024Article
- Tackling reference bias in genotyping by using founder sequences with PanVC 3.Bioinformatics advances · 2024Article
- Personalized Pangenome References.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
There is growing interest in using genetic variants to augment the reference genome into a graph genome, with alternative sequences, to improve read alignment accuracy and reduce allelic bias. While adding a variant has the positive effect of removing an undesirable alignment score penalty, it also increases both the ambiguity of the reference genome and the cost of storing and querying the genome index. We introduce methods and a software tool called FORGe for modeling these effects and prioritizing variants accordingly. We show that FORGe enables a range of advantageous and measurable trade-offs between accuracy and computational overhead.
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Registered trials
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.