ArticleBioinformatics advances2026
Pipeasm: a tool for automated large chromosome-scale genome assembly and evaluation.
Article in Bioinformatics advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 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
4 citing papers in PubMed.
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Diploid chromosome-level genome assembly of the Amazonian endemic morning glory Ipomoea cavalcantei D.F. Austin.Scientific data · 2026Article
- De Novo Chromosome-Level Assembly of the Endangered Pilocarpus Microphyllus Highlights Genomic Resources for Conservation and Sustainable Pilocarpine Extraction.Genome biology and evolution · 2026Article
- Ten quick tips for using the NIH Comparative Genomics Resource.PLoS computational biology · 2026Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Although high-quality chromosome-scale genome assemblies are feasible, assembling large ones remains complex and resource-intensive. This demands reproducible and automated workflows that not only implement current best practices efficiently but also allow for improvement alongside future updates to those standards. Results: We present Pipeasm, a Snakemake-based genome assembly pipeline containerized with Singularity. Pipeasm can use HiFi, ONT, and Hi-C data, automating read trimming, nuclear and mitogenome assembly, scaffolding, decontamination, and quality evaluation. Applied to four vertebrate species with distinct genomic characteristics, starting from a single command line and configuration file, it produced assemblies with scaffold L50 proportional to the expected chromosome and genome length, and up to 99.6% BUSCO completeness. Its output also includes detailed reports for each step, genome statistics, Hi-C maps, and files ready for curation. Availability and implementation: Pipeasm is available at https://github.com/itvgenomics/pipeasm, implemented in Python/Snakemake with Singularity, and runs on Unix-based systems.
Identifiers
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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.