Acacia protocols

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Acacia specifications

Information


Unique identifier OMICS_01116
Name Acacia
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Roche
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Gene W. Tyson <>

Publication for Acacia

Acacia in pipelines

 (5)
2018
PMCID: 5835077
PMID: 29535686
DOI: 10.3389/fmicb.2018.00295

[…] titanium. all the raw reads were deposited in the ncbi sequence read archive (sra) database under accession number of prjna403937., reads of these 4 gene fragments more than 400 bp were extracted by acacia software with each barcode on the forward primers (bragg et al., ). for ks and ad gene fragments, all the retrieved reads were trimmed to 400 bp from the forward primer site; for dtgd and 16s […]

2017
PMCID: 5523551
PMID: 28790984
DOI: 10.3389/fmicb.2017.01361

[…] on materials and methods., the reads of bacterial genes were trimmed to nearly equal sequence lengths (446 bp for 16s rrna, 440 bp for mxaf), amplicon pyrosequencing errors were corrected using acacia, and potential 16s rrna chimeric sequences were sorted out using the uchime algorithm implemented in usearch and the latest rdp gold database for high-quality 16s rrna gene reference sequences […]

2015
PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] before performing the error correction, if they consistently differ from the consensus at all conflict columns they cover and thus effectively incorporates a simpler repeat model than mised. acacia [], a tool developed for 454 pyrosequencing data (section ‘platform specific error correction’), also uses linkage between mismatches as in sga. however, it clusters and aligns run-length […]

2015
PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] before performing the error correction, if they consistently differ from the consensus at all conflict columns they cover and thus effectively incorporates a simpler repeat model than mised. acacia [], a tool developed for 454 pyrosequencing data (section ‘platform specific error correction’), also uses linkage between mismatches as in sga. however, it clusters and aligns run-length […]

2013
PMCID: 3634081
PMID: 23626688
DOI: 10.1371/journal.pone.0061463

[…] newbler software (version 2.5.3, roche) and returned as raw data in a standard flowgram file (.sff) format. raw data (.sff) was converted to.fasta and.qual files using mothur and denoised using acacia software . denoised sequences and metadata were submitted to mg-rast (http:/metagenomics.anl.gov) and are stored under project name ‘qemh’ - record numbers for each amplicon library are: […]


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Acacia in publications

 (62)
PMCID: 5914283
PMID: 29688220
DOI: 10.1038/sdata.2018.68

[…] in length, were removed. all of these processing steps were performed using qiime 1.9.0 (ref. ). to minimize a type of platform-dependent error, homopolymorphic error, denoising was conducted using acacia (ver. 1.53) and default parameters., low-quality reads were filtered using trimmomatic (ver. 0.35), with a minimum read length of 150 bp and nextera adapter sequence trimming options. reads […]

PMCID: 5835077
PMID: 29535686
DOI: 10.3389/fmicb.2018.00295

[…] titanium. all the raw reads were deposited in the ncbi sequence read archive (sra) database under accession number of prjna403937., reads of these 4 gene fragments more than 400 bp were extracted by acacia software with each barcode on the forward primers (bragg et al., ). for ks and ad gene fragments, all the retrieved reads were trimmed to 400 bp from the forward primer site; for dtgd and 16s […]

PMCID: 5835139
PMID: 29535763
DOI: 10.3389/fgene.2018.00062

[…] caporaso et al., ). sequences were assigned to their originating sample based on the attached barcode and filtered based on quality and length parameters. error correction was performed using acacia (bragg et al., ). clustering of sequences to an operational taxonomic unit at a 0.97 distance threshold performed using uclust (edgar, ). chimeric sequences were identified using chimera […]

PMCID: 5789842
PMID: 29382896
DOI: 10.1038/s41598-018-20302-7

[…] pooled together as well as those for intracellular dna. additional details on pyrosequencing analyses are reported in ., raw sequences were first subjected to homopolymer removal by means of the acacia tool with standard values, and subsequently quality-trimmed by means of the prinseq tool by removing sequences with a mean quality score <20 and further filtered to remove sequences shorter […]

PMCID: 5816780
PMID: 29368074
DOI: 10.1007/s10096-018-3193-y

[…] are available in the european nucleotide archive (http://www.ebi.ac.uk/ena) under study accession prjeb19937., pyrosequencing data were analysed using the qiime software package (v1.8) [] applying acacia [], usearch [], uclust [] and the silva 111 database [] for denoising, chimera removal, operational taxonomic unit (otu) picking and taxonomic classification, respectively. the obtained otu […]


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Acacia institution(s)
Advanced Water Management Centre, The University of Queensland, St. Lucia, QLD, Australia; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia; Commonwealth Scientific and Industrial Research Organisation Mathematics, Informatics and Statistics, QLD, Australia; School of Computing and Mathematics, University of Western Sydney, NSW, Australia; Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, Australia
Acacia funding source(s)
This project was supported by a PhD scholarship funded by the Commonwealth Scientific and Industrial Research Organisation Transformational Biology capability platform, by a Queen Elizabeth II Fellowship from the Australian Research Council (grant No. DP1093175) and by a strategic University of Queensland funding of the Australian Centre for Ecogenomics.

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