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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

Versioning


No version available

Documentation


Maintainer


  • person_outline Gene W. Tyson

Publication for Acacia

Acacia citations

 (67)
library_books

The fallopian tube microbiome: implications for reproductive health

2018
Oncotarget
PMCID: 5940370
PMID: 29765558
DOI: 10.18632/oncotarget.25059

[…] Amplicon sequences were length filtered and quality trimmed using Acacia, which also corrects homopolymer errors []. Sequences were assigned to their respective samples based on oligonucleotide barcodes using QIIME. Sequence clustering and operational taxonomic unit […]

library_books

Diversity of Gene Clusters for Polyketide and Nonribosomal Peptide Biosynthesis Revealed by Metagenomic Analysis of the Yellow Sea Sediment

2018
Front Microbiol
PMCID: 5835077
PMID: 29535686
DOI: 10.3389/fmicb.2018.00295

[…] After processing of the retrieved reads with Acacia software, 9995 KS reads, 4042 AD reads and 602 dTGD reads were obtained (Table ). The KS and AD reads were classified into OTUs at 90% identity, and the dTGD reads were classified into OTUs at […]

library_books

Genetic Markers Are Associated with the Ruminal Microbiome and Metabolome in Grain and Sugar Challenged Dairy Heifers

2018
Front Genet
PMCID: 5835139
PMID: 29535763
DOI: 10.3389/fgene.2018.00062

[…] (QIIME; 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 slayer […]

library_books

Analytical parameters and validation of homopolymer detection in a pyrosequencing based next generation sequencing system

2018
BMC Genomics
PMCID: 5822529
PMID: 29466940
DOI: 10.1186/s12864-018-4544-x

[…] lustering the flowgrams; for example Denoiser, which utilizes rank-abundance distributions, or PyroNoise/AmpliconNoise, which calculates a likelihood using empirically derived error distributions []. Acacia’s main focus is on HP sequences and the algorithm uses a dynamically updated cluster consensus when aligning reads []. Coral and ECHO are multiple alignment based techniques [], while HECTOR is […]

library_books

Extracellular DNA as a genetic recorder of microbial diversity in benthic deep sea ecosystems

2018
Sci Rep
PMCID: 5789842
PMID: 29382896
DOI: 10.1038/s41598-018-20302-7

[…] A were 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 tha […]

library_books

Association between duration of intravenous antibiotic administration and early life microbiota development in late preterm infants

2018
PMCID: 5816780
PMID: 29368074
DOI: 10.1007/s10096-018-3193-y

[…] 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 tab […]

Citations

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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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