ReviewGenome biology2021
Technology dictates algorithms: recent developments in read alignment.
Review in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled 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.
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.
Who cites it
61 citing papers in PubMed, 1 synthesis or guideline pooled it, 9 citations in OpenAlex.
- Packaging and containerization of computational methods.Nature protocols · 2024Pooled it
- Review
- Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.Genome research · 2026Article
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- Long-read sequencing for neurological disorders: opportunities, challenges, and future directions.Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology · 2026Review
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Singletrack: an algorithm for improving memory consumption and performance of gap-affine sequence alignment.Bioinformatics (Oxford, England) · 2026Article
- Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.bioRxiv : the preprint server for biology · 2026Article
- Multi-context seeds enable fast and high-accuracy read mapping.Genome biology · 2026Article
- Leveraging DNA repair mechanisms in genetically engineered biocontrol.Current opinion in insect science · 2026Review
- Reproducible Emu-Based Workflow for High-Fidelity Soil and Plant Microbiome Profiling on HPC Clusters.Bio-protocol · 2026Article
- RNA-Seq of Cultured Peripheral Blood Lymphocytes Improves Identification of Cryptic Splicing Defects in Rare Disease Diagnostics.Human mutation · 2026Article
- Panalyze: automated virus pangenome variation graph construction, analysis and annotation.Bioinformatics advances · 2026Article
- Article
- Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.bioRxiv : the preprint server for biology · 2025Article
- A closed-loop method for precise genome size estimation using HiFi reads.BMC genomics · 2025Article
- Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.bioRxiv : the preprint server for biology · 2025Article
- Panaln: indexing pangenome for read alignment.Bioinformatics (Oxford, England) · 2025Article
- Ensuring Biosecurity and Research Agility for Outbreak Response: A Researcher's Perspective on the Federal Nucleic Acid Screening Framework.Applied biosafety : journal of the American Biological Safety Association · 2025Article
- APALORD: An R-based tool for differential alternative polyadenylation analysis of long-read RNA-seq data.bioRxiv : the preprint server for biology · 2025Article
1 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 8 institutions in 4 countries.
Funding
Abstract
Aligning sequencing reads onto a reference is an essential step of the majority of genomic analysis pipelines. Computational algorithms for read alignment have evolved in accordance with technological advances, leading to today's diverse array of alignment methods. We provide a systematic survey of algorithmic foundations and methodologies across 107 alignment methods, for both short and long reads. We provide a rigorous experimental evaluation of 11 read aligners to demonstrate the effect of these underlying algorithms on speed and efficiency of read alignment. We discuss how general alignment algorithms have been tailored to the specific needs of various domains in biology.
Indexed as
Identifiers
What OpenQuestion holds
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.