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rolshausenlab_aspergillus_datepalm

Aspergillus tubingensis DFA genome sequencing and annotation

https://github.com/stajichlab/rolshausenlab_aspergillus_datepalm

Science Score: 44.0%

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    CITATION.cff file
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    Low similarity (3.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Aspergillus tubingensis DFA genome sequencing and annotation

Basic Info
  • Host: GitHub
  • Owner: stajichlab
  • License: mit
  • Language: Shell
  • Default Branch: main
  • Size: 59.6 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

Genome assembly and annotation of A. tubingensis strain DFA

Multiple assemblers were run (canu, flye, raven) and best assembly chosen based on [asm_stats.tsv] results. This template setup for running multiple samples is per the Stajich lab setup for running assembly and annotation.

See the [pipeline] folder for assembly, annotation, and statistics calculations.

Notes: * final assembly files used are called XX.pilon.fasta but the polishing step was actually POLCA used * scaffold10 was removed based on its identity to the subset of a match to scaffold6

Owner

  • Name: Jason Stajich Lab at UC Riverside
  • Login: stajichlab
  • Kind: organization
  • Email: jason.stajich@ucr.edu
  • Location: RIverside, CA

Evolutionary Genomics of Fungi projects, data and software

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: >-
  Genome assembly and annotation of Aspergillus tubingensis
  DFA from a date palm
message: >-
  If you use this dataset, please cite it using the metadata
  from this file.
type: dataset
authors:
  - given-names: Jason
    name-particle: E
    family-names: Stajich
    email: jason.stajich@ucr.edu
    affiliation: 'University of California, Riverside'
    orcid: 'https://orcid.org/0000-0002-7591-0020'
  - given-names: Vanessa
    family-names: Ashworth
    affiliation: 'University of California, Riverside'
    orcid: 'https://orcid.org/0000-0003-2561-3121'
  - family-names: Rolshausen
    given-names: Philippe
    orcid: 'https://orcid.org/0000-0002-6202-680X'
identifiers:
  - type: url
    value: >-
      https://github.com/stajichlab/RolshausenLab_Aspergillus_DatePalm
    description: Github repository
repository-code: >-
  https://github.com/stajichlab/RolshausenLab_Aspergillus_DatePalm
abstract: >-
  Genome assembly and annotation of Aspergillus tubingensis
  strain DFA isolated from a date palm. The genome was
  sequenced with Oxford Nanopore and Illumina technologies
  followed by assembly with Flye and polishing with POLCA.
  The genome was masked with RepeatModeler + RepeatMasker
  and annotated with Funannotate using available RNAseq for
  A. tubingensis and combination of gene prediction tools
  (Genemark.HMM+ET, SNAP, Augustus, CodingQuarry) and
  functional annotation assigned using Pfam, Interpro,
  Eggnog, and SignalP.
keywords:
  - Genome
  - Aspergillus
license: MIT
version: v1.0
date-released: '2024-07-15'

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