Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences.
Next 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.



With 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.



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.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
Jianwei
J
Zhang
Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
Dave
D
Kudrna
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Ting
T
Mu
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Weiming
W
Li
Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
Dario
D
Copetti
Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
Yeisoo
Y
Yu
Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
Jose Luis
JL
Goicoechea
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Yang
Y
Lei
Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
Rod A
RA
Wing
D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D012984:Software