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SolexaQA specifications

Information


Unique identifier OMICS_01078
Name SolexaQA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output format FASTQ, PDF, text
Biological technology Illumina, Life Technologies, Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
Matrix2png, GD graphics
Maintained Yes

Subtool


  • DynamicTrim

Versioning


No version available

Maintainer


  • person_outline Murray Cox

Publication for SolexaQA

SolexaQA citations

 (230)
library_books

TGFβ signaling related genes are involved in hormonal mediation during termite soldier differentiation

2018
PLoS Genet
PMCID: 5912798
PMID: 29641521
DOI: 10.1371/journal.pgen.1007338

[…] deposited in the ddbj sequence read archive (dra) database under accession numbers dra006300., the quality of all reads was checked by the fastqc program [], and low quality reads were removed by solexaqa software []. adapter sequences were removed using the cutadapt program []. cleaned reads were mapped to genome sequence data (gene model ogsv2.2; []) using tophat v2.0.8 software […]

library_books

Phenotypic and Genotypic Characterization of Enterobacteriaceae Producing Oxacillinase 48–Like Carbapenemases, USA

2018
PMCID: 5875285
PMID: 29553324
DOI: 10.3201/eid2404.171377

[…] and sequenced with miseq v2.0 (illumina, san diego, ca, usa). we filtered raw illumina sequencing reads for quality (average >q20) and discarded trimmed reads >50 bp from the dataset by using solexaqa version 3.1 (). we then assembled clean reads into contigs by using spades version 3.1.0 and 4 k-mer sizes (k = 41, 79, 85, and 97) (). afterward, we mapped trimmed reads back […]

library_books

Comparative Transcriptomics Among Four White Pine Species

2018
PMCID: 5940140
PMID: 29559535
DOI: 10.1534/g3.118.200257

[…] and trimming. the raw reads were trimmed and cleaned with sickle requiring a minimum read length of 45bp and a minimum quality score of 33 (). trimmed reads were subsequently processed with the solexaqa package to visualize overall quality and remove additional outliers (). following quality control, reads were combined between libraries of the same species and run as a single assembly […]

library_books

Draft Genome Sequences of Endophytic Isolates of Klebsiella variicola and Klebsiella pneumoniae Obtained from the Same Sugarcane Plant

2018
Genome Announc
PMCID: 5864947
PMID: 29567733
DOI: 10.1128/genomeA.00147-18

[…] a total of 4,706,652 paired-end reads in k. variicola kvmx2 and 2,562,748 paired-end reads in k. pneumoniae kpmx1 with a length of 150 bp were obtained. quality-based trimming was performed with the solexaqa software, and de novo assembly was done with spades version 3.1.1. the contigs were subjected to a scaffolding process with sspace version 2.0. for k. variicola kvmx2 and k. pneumoniae […]

library_books

HIV exposure, early life feeding practices and delivery mode impacts on faecal bacterial profiles in a South African birth cohort

2018
Sci Rep
PMCID: 5864830
PMID: 29567959
DOI: 10.1038/s41598-018-22244-6

[…] (15% phix) was added at 4 pm. the denatured library was loaded to the illumina® miseqtm platform as per manufacturer’s instructions., we assessed sequencing quality of fastq files using fastqc and solexaqa. we then merged forward and reverse sequences using usearch7 fastq_mergepairs (fastq_maxdiffs set to 3), followed by quality filtering using usearch7 fastq_filter (sequences truncated to 250 […]

library_books

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

2018
Sci Rep
PMCID: 5851996
PMID: 29540790
DOI: 10.1038/s41598-018-22817-5

[…] from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and sugar. after confirming the lack of technical errors in the miseq sequencing, low-quality tails were trimmed from each read using dynamictrim.pl from the solexaqa software package with a cut-off threshold set at a phred score of 10 (=10−1 error rate). the tail-trimmed pair-end reads were assembled using the software flash […]


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SolexaQA institution(s)
Institute of Molecular BioSciences, Massey University, New Zealand; The Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand; The Bio-Protection Research Centre, New Zealand; Institute of Veterinary, Animal and Biomedical Sciences, Massey University, New Zealand; Massey Genome Service, Massey University New Zealand

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