ArticleBioinformatics (Oxford, England)2022
PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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
9 citing papers in PubMed, 11 citations in OpenAlex.
- BCAR: a fast and indel-tolerant barcode-sequence mapper.Bioinformatics (Oxford, England) · 2026Article
- BCAR: A fast and general barcode-sequence mapper for correcting sequencing errors.bioRxiv : the preprint server for biology · 2026Article
- Variant scoring tools for deep mutational scanning.Molecular systems biology · 2025Review
- Multiplex and multimodal mapping of variant effects in secreted proteins via MultiSTEP.Nature structural & molecular biology · 2025Article
- Multiplex, multimodal mapping of variant effects in secreted proteins.bioRxiv : the preprint server for biology · 2025Article
- Deep mutational scanning of CYP2C19 in human cells reveals a substrate specificity-abundance tradeoff.Genetics · 2024Article
- Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries.Bioinformatics (Oxford, England) · 2024Article
- Pacybara: Accurate long-read sequencing for barcoded mutagenized allelic libraries.bioRxiv : the preprint server for biology · 2023Article
- A universal sequencing read interpreter.Science advances · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
summaryUse of PacBio sequencing for characterizing barcoded libraries of genetic variants is on the rise. However, current approaches in resolving PacBio sequencing artifacts can result in a high number of incorrectly identified or unusable reads. Here, we developed a PacBio Read Alignment Tool (PacRAT) that improves the accuracy of barcode-variant mapping through several steps of read alignment and consensus calling. To quantify the performance of our approach, we simulated PacBio reads from eight variant libraries of various lengths and showed that PacRAT improves the accuracy in pairing barcodes and variants across these libraries. Analysis of real (non-simulated) libraries also showed an increase in the number of reads that can be used for downstream analyses when using PacRAT. AVAILABILITY AND IMPLEMENTATION: PacRAT is written in Python and is freely available (https://github.com/dunhamlab/PacRAT). SUPPLEMENTARY INFORMATION: Supplemental data are available at Bioinformatics online.
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.