ArticleBioinformatics (Oxford, England)2025
Agptools: a utility suite for editing genome assemblies.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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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.
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Who cites it
2 citing papers in PubMed.
- Programmed DNA elimination was present in the last common ancestor ofbioRxiv : the preprint server for biology · 2026Article
- Genomic resources for comparative analyses of obligate avian brood parasitism.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
summaryThe AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how these components are assembled into larger pieces like scaffolds or chromosomes. For this reason, many scaffolding software pipelines output assemblies in this format. However, although many programs for assembling and scaffolding genomes read and write this format, there is currently no published software for making edits to AGP files when performing assembly curation. We present agptools, a suite of command-line programs that can perform common operations on AGP files, such as breaking and joining sequences, inverting pieces of assembly components, assembling contigs into larger sequences based on an AGP file, and transforming between coordinate systems of different assembly layouts. Additionally, agptools includes an API that writers of other software packages can use to read, write, and manipulate AGP files within their own programs. AVAILABILITY AND IMPLEMENTATION: Source code and binaries freely available for download at https://github.com/WarrenLab/agptools, implemented in Python and supported on all operating systems.
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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.