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


Add your version

Maintainer


  • person_outline Murray Cox <>

SolexaQA article

SolexaQA citations

 (12)
2017
PMCID: 5576253

[…] their 5′ ends using the rna-seq data., the rna-seq reads were subjected to the trimming of low-quality (less than 10 in the phred quality score; [31]) and short (less than 20 bp) reads with solexaqa [32]. the in-house blastn search (e-value cutoff: 1e-5) was then conducted with the mtdna sequence of an rna-sequenced individual as a query and the rna-seq reads after trimming […]

2017
PMCID: 5657738

[…] to higher accuracy than methods where only 1 nucleotide is present in the reaction mix at a time. the next procedure is data handling, which contains sequence quality check and data analysis. solexaqa is a perl-based software package that calculates quality statistics and creates visual representations of data quality from fastq files generated by illumina second-generation sequencing […]

2016
PMCID: 5103457

[…] a stepwise filtering pipeline (fig. 1) was used to identify putative lncrnas from 12 rna-seq datasets. (1) low-quality (phred score < 20) and short (length < 30 bp) reads were trimmed using solexaqa [14]. the trimmed and size selected reads were then mapped to the nmr’s genome using tophat [50]. (2) aligned reads were assembled and merged by cufflinks and cuffmerge, and then noncoding […]

2016
PMCID: 5099574

[…] library in a single run to produce pair end reads with length of 2 × 300 bp. the first library was clustered to a density of 1339 k/mm2, the second one to 1066 k/mm2., raw reads were trimmed using a solexaqa package 2.237 with minimum phred 10 quality value of 30 and minimum length of 100 bp. all reads obtained in this work were deposited in the national center for biotechnology information […]

2016
PMCID: 4860700

[…] using the illumina hiseq 2000 at beijing genomics institute (shenzhen, china). over 4.4 gb of paired-end 100-bp reads were generated from each sample. low-quality bases were trimmed using the dynamictrim program in solexaqa (cox et al. 2010) with a phred quality score cutoff of 20. all the reads were used for de novo transcriptome assembling with trinity (grabherr et al. 2011), […]

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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