SolexaQA pipeline

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 <>

Publication for SolexaQA

SolexaQA IN pipelines

 (21)
2017
PMCID: 5576253
PMID: 28851277
DOI: 10.1186/s12864-017-4080-0

[…] 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: 5601042
PMID: 28955355
DOI: 10.3389/fpls.2017.01559

[…] tophat v2.0.9 (trapnell et al., 2009). raw reads were preprocessed to remove adaptors using an in-house developed perl script. after filtering out low-quality (lowest base score < 30) reads using solexaqa v3.1.3 (cock et al., 2010). the multi-mapped read correction and fragment bias correction options of cufflinks v2.1.1 (trapnell et al., 2010) were used. gene expression levels were reported […]

2017
PMCID: 5865777
PMID: 28849048
DOI: 10.3892/mmr.2017.7351

[…] generated with 100 bp in the forward and reverse direction. sequencing adapter sequences were removed with cutadapt (http://code.google.com/p/cutadapt/). the length of each read was trimmed using solexaqa (http://solexaqa.sourceforge.net/) with the options ‘-b -p 0.05’. read pairs with either reads <35 bp were removed with a custom python script. the high-quality reads were then aligned […]

2017
PMCID: 5865777
PMID: 28849048
DOI: 10.3892/mmr.2017.7351

[…] 100 bp in the forward and reverse direction. sequencing adapter sequences were removed with cutadapt (http://code.google.com/p/cutadapt/). the length of each read was trimmed using solexaqa (http://solexaqa.sourceforge.net/) with the options ‘-b -p 0.05’. read pairs with either reads <35 bp were removed with a custom python script. the high-quality reads were then aligned to the human genome […]

2016
PMCID: 4783988
PMID: 26907259
DOI: 10.3390/ijms17020259

[…] the national center for biotechnology information (ncbi) sequence reads archive (sra) with accession numbers srp066131 (xoo kacc10331) and srp066133 (xoo hb1009). sequencing reads were processed by solexaqa software [50] to control the quality of raw data. the trimmed reads were mapped to the xoo kacc 10331 genome (ncbi accession no. nc_006834) using bowtie aligner […]

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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