A5 pipeline

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

Versioning


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Documentation


Maintainers


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

Publications for A5

A5 IN pipelines

 (11)
2018
PMCID: 5766633
PMID: 29330501
DOI: 10.1038/s41598-017-18934-2

[…] using the nextera xt dna library preparation kit (illumina) and sequenced with the miniseq mid output kit (illumina). the illumina short reads of long-pcr fragments were assembled using the a5-miseq program54, followed by verification of the 5′ and 3′ end regions containing ltr regions using sanger sequencing data. short servs (<~2 kb; svl id; 13c, 15f, 22e, 26) were sequenced […]

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

[…] as part of a large-scale watershed metagenomics project, bioproject id: 2878401., trimmomatic version 0.32 (bolger et al., 2014) was used to remove adapters using the sequences packaged with the a5-miseq assembly pipeline (coil et al., 2015). low quality and short sequences (<75 nt) were discarded. sequences were then assembled using pandaseq (masella et al., 2012); unassembled pairs […]

2017
PMCID: 5391416
PMID: 28408678
DOI: 10.1128/genomeA.00163-17

[…] size of 450 bp (paired-end), and the second had an insert size of 8,000 bp (mate-pair). sequencing produced 18 million reads (~100-fold coverage) of 120 bp each. the fragments were assembled in a5-miseq (5) with default settings and sspace (6). the final assembly has seven scaffolds, with a maximum length of 5,775,319 bp. the genome was annotated using the ncbi prokaryotic genome annotation […]

2017
PMCID: 5454213
PMID: 28572330
DOI: 10.1128/genomeA.00466-17

[…] genome; the first had an insert of 450 bp (paired-end), and the second 8,000 bp (mate pair). sequencing produced 18 million (~70-fold coverage) reads of 120 bp each. the fragments were assembled in a5-miseq (9), with default settings, and sspace (10). the final assembly has 28 scaffolds, with an n50 of 2,132,757 bp. the genome was annotated using the ncbi prokaryotic genome annotation pipeline […]

2017
PMCID: 5629057
PMID: 28983000
DOI: 10.1128/genomeA.01073-17

[…] 300 bp on an illumina miseq platform. the quality metrics of the reads were determined by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). the sequence data were assembled using the a5-miseq assembler (17), and the genome sequence was annotated via the ncbi prokaryotic genome annotation pipeline (18). the contigs were reordered with r2cat (19). the genome statistics are shown in […]

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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