skewer pipeline

skewer specifications

Information


Unique identifier OMICS_02106
Name skewer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for skewer

skewer citations

 (5)
2018
PMCID: 5833356

[…] were performed in terms of the manufacture’s manual. a computational pipeline was employed to process rna-sequencing data. clean reads were obtained after the raw reads were filtered with adaptor skewer78, and sequencing data were mapped to mouse genome mm10 refseq with tophat version 2.0.13 with default parameters79. gfold version 1.1.2 was used to produce biologically meaningful rankings […]

2016
PMCID: 5033589

[…] were used for each strain in each condition. polya-selected library preparation and rna-seq was carried out by bgi (www.genomics.cn/en) using illumina hiseq2500. raw rna-seq reads were trimmed using skewer v0.1.117 and aligned to the respective cgob genome using tophat2 v2.0.12 [54, 55]. aligned rna-seq data was visualized using jbrowse v1.11.2 [56]. raw rna-seq data is available at the ncbi […]

2016
PMCID: 5027350

[…] transfected with sirna negative control or crispld2 knockdown, in technical duplicates. the reads from resulting rna‐seq output fastq files were trimmed of the truseq adapter sequences using skewer (jiang et al. 2014) with default parameters. fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to visualize phred quality scores for initial quality control. […]

2016
PMCID: 4924338

[…] for each of the 72 samples and sequenced with illumina hiseq 2000 for 100 bp for both pair ends. the data has been submitted to ncbi sra as bioproject prjna293671. read data was trimmed with skewer [95] and quality controlled with fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). reads were aligned with to t. reesei genome version 2.0 [91] retrieved with gff annotations […]

2015
PMCID: 4457057

[…] and 600 bp, respectively. the sequencing was performed on an illumina miseq platform using a miseq reagent kit v3, 600 cycles. a total of 2,931,855 × 2 × 301 bp generated reads were subjected to the skewer (5) program (version 0.1.123) with a quality threshold of 9 and an error threshold of 0.25 for adapter trimming, and then de novo assembled using the abyss program (6) (version 1.5.2) […]

skewer institution(s)
Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Huixinli, Beijing, China

skewer review

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Fabien Pichon

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Desktop
The best trimmer I used so far because it takes indels into account, which is not the case for most of trimmers. Furthermore you can specify a ratio for mismatches and indels separately, which is very smart. I recommend !