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Protocols

A5 specifications

Information


Unique identifier OMICS_00005
Name A5
Alternative name A5-miseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained No

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Publications for A5

A5 citations

 (156)
library_books

Near full length 16S rRNA gene next generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae

2018
Microbiome
PMCID: 5935925
PMID: 29729663
DOI: 10.1186/s40168-018-0463-y

[…] illumina reads was performed as per the method of burke and darling []; scripts are available on github in the koadman/longas repository: https://github.com/koadman/longas. briefly, inside the a5-miseq pipeline, the reads first undergo adapter and quality trimming with trimmomatic [], then error correction with the sga k-mer correction algorithm []. next the corrected reads are assembled […]

library_books

Genome based analysis of Carbapenemase producing Klebsiella pneumoniae isolates from German hospital patients, 2008 2014

2018
PMCID: 5930415
PMID: 29744043
DOI: 10.1186/s13756-018-0352-y

[…] trimmomatic 16 (version 0.32, parameters: illuminaclip off, maxinfo 50:0.8, leading 3, trailing 3, crop off, headcrop off, minlen 36, avgqual off). trimmed reads were de novo assembled using a5-miseq (version 20,150,522) []., wgs data of all isolates were analysed using resfinder [], plasmidfinder and the mlst tool [] provided by the centre for genomic epidemiology […]

library_books

Human Activity Determines the Presence of Integron Associated and Antibiotic Resistance Genes in Southwestern British Columbia

2018
Front Microbiol
PMCID: 5938356
PMID: 29765365
DOI: 10.3389/fmicb.2018.00852

[…] and are available as part of a large-scale watershed metagenomics project, bioproject id: 287840., trimmomatic version 0.32 () was used to remove adapters using the sequences packaged with the a5-miseq assembly pipeline (). low quality and short sequences (<75 nt) were discarded. sequences were then assembled using pandaseq (); unassembled pairs were retained. de novo assembly […]

library_books

Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

2018
BMC Genomics
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] creek (4634) and robertson (1669) indicating that assembly fragmentation is potentially caused by greater haplotype diversity and quasi-species in the goon nure isolate. the assembly pipeline used, a5-miseq, was designed to assemble haploid genomes of clonal, axenically-cultured microbes. when substantial genomic polymorphism is likely to be present in the data, the pipeline produces […]

library_books

Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan

2018
Genome Announc
PMCID: 5920169
PMID: 29700164
DOI: 10.1128/genomeA.00362-18

[…] on a hiseq x ten sequencing platform (illumina, san diego, ca, usa) at the beijing genomics institute (shenzhen, china)., raw reads were preprocessed using soapnuke () and assembled using the a5-miseq pipeline (). contigs were binned and clustered on the basis of tetranucleotide frequency, g+c content, and differential coverage using binsanity (). reads mapping to the resulting bin […]

call_split

Mansonella ozzardi mitogenome and pseudogene characterisation provides new perspectives on filarial parasite systematics and CO 1 barcoding

2018
Sci Rep
PMCID: 5906601
PMID: 29670192
DOI: 10.1038/s41598-018-24382-3
call_split See protocol

[…] reads corresponding to human-host dna were filtered out by mapping them against a human reference genome (accession number: gca_000001405.19). the m. ozzardi mitogenome was assembled with the a5-miseq pipeline. mapping and short read post-processing was performed using bowtie2 software and samtools utilities, respectively. the prediction of protein-coding genes, rrnas and trnas was done […]


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A5 institution(s)
Genome Center, University of California Davis, Davis, CA, USA; ithree institute, University of Technology Sydney, NSW, Australia
A5 funding source(s)
Supported in part by a collaborative agreement with the NSW Department of Primary Industries.

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