A5 protocols

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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 Yes

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Documentation


Maintainers


  • person_outline Aaron E. Darling <>
  • person_outline Aaron E. Darling <>

Publications for A5

A5 in pipelines

 (30)
2018
PMCID: 5764942
PMID: 29326218
DOI: 10.1128/genomeA.01435-17

[…] genomic dna (gdna) of b. tribocorum strains l103 and c635 were sequenced on a miseq sequencer (illumina, inc., san diego, ca, usa) using the paired-end strategy. raw reads were assembled with a5-miseq software (). genome and subsystem-based annotations were performed by rapid annotation using subsystem technology (rast) (, ). trna gene detection was performed using the trnascan-se 2.0 […]

2018
PMCID: 5880886
PMID: 29636734
DOI: 10.3389/fmicb.2018.00538

[…] ). 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 […]

2018
PMCID: 5906601
PMID: 29670192
DOI: 10.1038/s41598-018-24382-3

[…] 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 […]

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

[…] coverage using binsanity (). reads mapping to the resulting bin were extracted using burrows-wheeler aligner (bwa) () and samtools (). reassembly and final scaffolding were performed using the a5 miseq pipeline (). the resulting scaffold was refined to reduce contamination on the basis of tetranucleotide frequency, g+c content, and differential coverage using refinem (). checkm () reported […]

2018
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 […]


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A5 in publications

 (141)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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