التفاصيل البيبلوغرافية
| العنوان: |
Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny |
| المؤلفون: |
Catchen, Julian, Amores, Angel, Bassham, Susan |
| سنة النشر: |
2020 |
| المجموعة: |
Zenodo |
| مصطلحات موضوعية: |
chromonomer, genome assembly, genetic map, sygnathus scovelli, Xiphophorus maculatus, Notothenia coriiceps, Restriction site-associated DNA sequencing (RADSeq) |
| الوصف: |
The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a "chromonome". We demonstrate Chromonomer's performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality. ; Each integration includes a shell script (chrr.sh) outlining how the chromonomer software was executed. Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001AwardTest Number: 1645087Funding provided by: National Science Foundation**Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001AwardTest Number: 1543383Funding provided by: National Institutes of HealthCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000002AwardTest Number: R01 ODO11116Funding provided by: National Institutes of HealthCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000002AwardTest ... |
| نوع الوثيقة: |
dataset |
| اللغة: |
unknown |
| العلاقة: |
https://zenodo.org/communities/dryadTest; https://zenodo.org/record/4002655Test; https://doi.org/10.5061/dryad.gtht76hjmTest; oai:zenodo.org:4002655 |
| DOI: |
10.5061/dryad.gtht76hjm |
| الإتاحة: |
https://doi.org/10.5061/dryad.gtht76hjmTest
https://zenodo.org/record/4002655Test |
| حقوق: |
info:eu-repo/semantics/openAccess ; https://creativecommons.org/publicdomain/zero/1.0/legalcodeTest |
| رقم الانضمام: |
edsbas.276290F5 |
| قاعدة البيانات: |
BASE |
