ArticleBioinformatics (Oxford, England)2016
Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies.Scientific data · 2023Article
- Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice.Plant physiology · 2023Article
- Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics.G3 (Bethesda, Md.) · 2022Article
- The chromosome-scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis.Plant biotechnology journal · 2021Article
- Eight soybean reference genome resources from varying latitudes and agronomic traits.Scientific data · 2021Article
- Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice.The Plant journal : for cell and molecular biology · 2020Article
- A platinum standard pan-genome resource that represents the population structure of Asian rice.Scientific data · 2020Article
- Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis.GigaScience · 2018Article
- A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes.GigaScience · 2018Article
- Article
- Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.Plant biotechnology journal · 2017Article
- Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data.Scientific data · 2016Article
- Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationNext generation sequencing technologies have revolutionized our ability to rapidly and affordably generate vast quantities of sequence data. Once generated, raw sequences are assembled into contigs or scaffolds. However, these assemblies are mostly fragmented and inaccurate at the whole genome scale, largely due to the inability to integrate additional informative datasets (e.g. physical, optical and genetic maps). To address this problem, we developed a semi-automated software tool-Genome Puzzle Master (GPM)-that enables the integration of additional genomic signposts to edit and build 'new-gen-assemblies' that result in high-quality 'annotation-ready' pseudomolecules.
resultsWith GPM, loaded datasets can be connected to each other via their logical relationships which accomplishes tasks to 'group,' 'merge,' 'order and orient' sequences in a draft assembly. Manual editing can also be performed with a user-friendly graphical interface. Final pseudomolecules reflect a user's total data package and are available for long-term project management. GPM is a web-based pipeline and an important part of a Laboratory Information Management System (LIMS) which can be easily deployed on local servers for any genome research laboratory. AVAILABILITY AND IMPLEMENTATION: The GPM (with LIMS) package is available at https://github.com/Jianwei-Zhang/LIMS CONTACTS: jzhang@mail.hzau.edu.cn or rwing@mail.arizona.eduSupplementary information: Supplementary data are available at Bioinformatics online.
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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.