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A5 specifications


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 Yes


No version available



  • person_outline Aaron E. Darling
  • person_outline Aaron E. Darling

Publications for A5

A5 citations


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

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

[…] tagged 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 wi […]


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

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

[…] Genome assembly was achieved with raw reads using the A5-miseq (v2015–05-22) pipeline []. Levels of remaining host DNA were assessed and filtered using BioBloomTools [] and the B. taurus genome sequence []. Whole genome alignments were performed using pr […]


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

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

[…] equencing 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 were ex […]


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

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

[…] raries. 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 us […]


Complete Mitochondrial Genome of Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) and Phylogenetic Analysis of Pentatomomorpha Species

PMCID: 5905379
PMID: 29718506
DOI: 10.1093/jisesa/iey031

[…] ina). The target insert size was 500 bp. The adapter sequences were removed and low-quality bases were trimmed using the Trimmomatic version 0.36 (). These targeted sequences were assembled using the A5-miseq v2015022 () and Spades v3.9.0 () software. […]


Retrospective Analysis of Bacterial Cultures Sampled in German Chicken Fattening Farms During the Years 2011–2012 Revealed Additional VIM 1 Carbapenemase Producing Escherichia coli and a Serologically Rough Salmonella enterica Serovar Infantis

Front Microbiol
PMCID: 5880886
PMID: 29636734
DOI: 10.3389/fmicb.2018.00538

[…] al., ). In addition, the E. coli recipient strain NEB®10-beta was sequenced. The raw-data were de novo assembled using SPAdes (Bankevich et al., ). An additional assembly was performed for G-268-2 by A5-miseq (v. 0.0.9 beta; default parameters) using trimmed raw reads (Trimmomatic: v. 0.0.9; default parameters except maxinfo 15:0.5) (Bolger et al., ; Coil et al., ). Resistance genes, virulence gen […]

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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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