SolexaQA protocols

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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


Add your version

Maintainer


  • person_outline Murray Cox <>

Publication for SolexaQA

SolexaQA in pipelines

 (42)
2018
PMCID: 5845709
PMID: 29559983
DOI: 10.3389/fpls.2018.00244

[…] sequencing reads from all of the three biological replicates were pre-processed, and cutadapt was used to remove adapters (martin, ). the raw reads were filtered into clean reads using solexaqa (those with ≤60 bp were discarded) (cox et al., ). then, using the tophat 2.0 program (trapnell et al., ), the assembled reads were mapped to the wheat genome: […]

2017
PMCID: 5217272
PMID: 28056773
DOI: 10.1186/s12864-016-3417-4

[…] pair paired end reads., sequencing reads were first trimmed for sequencing adaptor and then for quality at phred score of q20. only paired end reads longer than 50 nucleotides were kept using the solexaqa package []. reads were mapped against the mouse genome version 10 using tophat [] and bowtie 2 []. read count were summarized at the transcript level using refseq annotation from the mapping […]

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; []) and short (less than 20 bp) reads with solexaqa []. 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 as a database. […]

2017
PMCID: 5578835
PMID: 28860237
DOI: 10.1128/genomeA.00745-17

[…] was sequenced using the illumina hiseq platform (2 × 300 bp paired-end reads). a total of 814,835 reads were obtained, and quality trimming and error correction of the reads were performed using a dynamictrim (solexaqa++) () perl script. reads were assembled using spades version 3.5.0 (), and the draft genome resulted in 91 contigs with a total length of 5,472,253 bp. the largest contig […]

2017
PMCID: 5589524
PMID: 28883130
DOI: 10.1128/genomeA.00746-17

[…] and 5 µg of genomic dna was sequenced using the illumina hiseq platform (2 × 300 bp paired-end) approach. we obtained a total of 9,447,636 reads that were quality trimmed and error corrected using dynamictrim (solexaqa++) perl script (). reads were assembled using spades version 3.5.0 (). the draft genome consists of 54 contigs with a total length of 6,375,895 bp. the largest contig […]


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SolexaQA in publications

 (207)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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