PMID- 27318200
OWN - NLM
STAT- MEDLINE
DCOM- 20170815
LR  - 20181202
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 32
IP  - 20
DP  - 2016 Oct 15
TI  - Genome puzzle master (GPM): an integrated pipeline for building and editing 
      pseudomolecules from fragmented sequences.
PG  - 3058-3064
AB  - MOTIVATION: 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. RESULTS: 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. 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.
CI  - (c) The Author 2016. Published by Oxford University Press.
FAU - Zhang, Jianwei
AU  - Zhang J
AD  - 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.
FAU - Kudrna, Dave
AU  - Kudrna D
AD  - Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, 
      University of Arizona, Tucson, AZ 85721, USA.
FAU - Mu, Ting
AU  - Mu T
AD  - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural 
      University, Wuhan 430070, China.
FAU - Li, Weiming
AU  - Li W
AD  - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural 
      University, Wuhan 430070, China.
FAU - Copetti, Dario
AU  - Copetti D
AD  - 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 Banos, Laguna, Philippines.
FAU - Yu, Yeisoo
AU  - Yu Y
AD  - Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, 
      University of Arizona, Tucson, AZ 85721, USA.
FAU - Goicoechea, Jose Luis
AU  - Goicoechea JL
AD  - Arizona Genomics Institute and BIO5 Institute, School of Plant Sciences, 
      University of Arizona, Tucson, AZ 85721, USA.
FAU - Lei, Yang
AU  - Lei Y
AD  - National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural 
      University, Wuhan 430070, China.
FAU - Wing, Rod A
AU  - Wing RA
AD  - 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 Banos, Laguna, Philippines.
LA  - eng
PT  - Journal Article
DEP - 20160617
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
SB  - IM
MH  - Genome
MH  - *Genomics
MH  - *High-Throughput Nucleotide Sequencing
MH  - *Software
PMC - PMC5048067
EDAT- 2016/06/19 06:00
MHDA- 2017/08/16 06:00
PMCR- 2016/06/17
CRDT- 2016/06/19 06:00
PHST- 2016/04/07 00:00 [received]
PHST- 2016/06/06 00:00 [accepted]
PHST- 2016/06/19 06:00 [pubmed]
PHST- 2017/08/16 06:00 [medline]
PHST- 2016/06/19 06:00 [entrez]
PHST- 2016/06/17 00:00 [pmc-release]
AID - btw370 [pii]
AID - 10.1093/bioinformatics/btw370 [doi]
PST - ppublish
SO  - Bioinformatics. 2016 Oct 15;32(20):3058-3064. doi: 10.1093/bioinformatics/btw370. 
      Epub 2016 Jun 17.