CodingQuarry statistics

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Associated diseases

Associated diseases

CodingQuarry specifications

Information


Unique identifier OMICS_07694
Name CodingQuarry
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Parallelization OpenMP
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Alison Testa <>

Publication for CodingQuarry

CodingQuarry in pipelines

 (2)
2017
PMCID: 5683368
PMID: 29158777
DOI: 10.1186/s13068-017-0956-0

[…] was performed ab initio using the hmm-based algorithm glimmer v. 3.02 [], which was trained using the genome of uncinocarpus reesii (downloaded from jgi, []). additionally, the software tool codingquarry [] was used for an evidence-based method of gene finding, where exon–intron boundaries were determined using the mapped mrna-seq reads. for functional gene annotation, coding dna […]

2017
PMCID: 5683368
PMID: 29158777
DOI: 10.1186/s13068-017-0956-0

[…] with a q score ≥ 30, and was greater than 88% in both cases. the final genome size of the assembly was 24.96 mb comprising 797 scaffolds. the output of two gene prediction algorithms (glimmer and codingquarry) was combined into a single gene model and yielded 9437 protein-coding genes with an average length of 388 amino acids. both the size of the assembled m. cinnamomea sequence […]


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CodingQuarry in publications

 (11)
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] [] using a combination of supporting protein and transcript alignments and ab initio predictions on a repeat masked genome, with minimum intron length of 10 bp and weights for ab initio prediction codingquarry:1, genemark.hmm:1, bfp protein exonerate:2., gene predictions for the m4 and bfp mitochondrial genomes were made using mitos webserver [] and refined based on blast versus […]

PMCID: 5915480
PMID: 29720997
DOI: 10.3389/fgene.2018.00130

[…] using hisat2 v2.0.4 () specifying a max intron length of 5 kb and the “dta-cufflinks” option to report alignments tailored for cufflinks input. cufflinks-guided annotations were generated using codingquarry pathogen-mode (cqpm, ) which were later provided to augustus (; ) as hints. intron position hints were extracted from the mapped rnaseq reads using the bam2hints utility provided […]

PMCID: 5887033
PMID: 29622620
DOI: 10.1128/genomeA.01414-17

[…] was 48.91%, as assessed by quast (). the genome of phlebia brevispora was used as a gene-finding trainer for the hmm-based algorithm glimmer (version 3.02) (). mapped mrna-seq reads were used by the codingquarry software tool () for an evidence-based method of gene finding. using the two methods combined, gene models for 13,785 genes were obtained. gene models encoding lignin degradation-related […]

PMCID: 5821087
PMID: 29463659
DOI: 10.1128/mBio.02275-17

[…] at our study’s github respository., we annotated genes on primary contigs and haplotigs independently. we combined rna-seq-guided ab initio predictions by using codingquarry v2.0 () and braker v1.9 () with de novo transcriptome assembly approaches of trinity v2.2.0 () and pasa v2.0.1 (). gene models were unified using evidencemodeler v1.1.1 () […]

PMCID: 5815587
PMID: 29451893
DOI: 10.1371/journal.pone.0191824

[…] as required. quast [] was used to summarise assembly statistics and busco [] was used to assess completeness of gene space within the assembly. gene prediction was performed using braker1 and codingquarry [,] and functional annotations predicted for these proteins using interproscan []. sequence data and annotated genomes were deposited at ddbj/embl/genbank within bioprojects prjna344737 […]


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CodingQuarry institution(s)
Centre for Crop and Disease Management, Department of Environment and Agriculture, School of Science, Curtin University, Bentley, WA, Australia

CodingQuarry review

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Anonymous user #1548

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Somewhat biased, but there is currently no alternative RNA-seq-based gene-prediction tool that adequately deals with overlapping UTR support from RNA-seq reads.