skewer statistics

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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 in pipelines

 (13)
2018
PMCID: 5833356
PMID: 29362488
DOI: 10.1038/s41419-017-0046-z

[…] 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 skewer, and sequencing data were mapped to mouse genome mm10 refseq with tophat version 2.0.13 with default parameters. gfold version 1.1.2 was used to produce biologically meaningful rankings […]

2017
PMCID: 5299730
PMID: 28178932
DOI: 10.1186/s12864-017-3529-5

[…] variation in cucumber, we retrieved 115 published resequences [] of several varieties, publicly available at ena [] (study: prjna171718). the fastq files were trimmed and filtered with skewer [] and aligned to the gy14 reference genome with bwa mem []. large deletions were detected with delly []. pavs were retained when ten or more paired end reads with a minimum mapping quality […]

2017
PMCID: 5340393
PMID: 28267806
DOI: 10.1371/journal.pone.0173421

[…] nucleotides read size was done with illumina hiseq 4000 sequencing platform. raw sequencing data was processed by the illumina base-calling pipeline., adaptor and low-quality bases were trimmed with skewer (version: 0.1.126) [], and the clean reads were aligned to the reference pig genome (sscrofa10.2) downloaded from ensemble (www.ensembl.org) with bwa mem (version:0.7.12) []. duplicated reads […]

2017
PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] 59 million paired end reads from two individuals (1 male and 1 female) were error corrected using rcorrector version 1.0.2. adapters, as well as bases with a phred score <2 were trimmed using skewer 0.2.2, and assembly was carried out using trinity version 2.2.0, binpacker version 1.0, and shannon version 0.0.2, after which the resultant transcriptomes were merged using the software […]

2017
PMCID: 5565190
PMID: 28793306
DOI: 10.1371/journal.pntd.0005752

[…] hiseq 3000 instrument (150 bp paired-end). an approach similar to a previous s. stercoralis population study [] was used to analyze the whole genome data. in brief, raw reads were trimmed with skewer [] (version 0.1.123; -q 30 -q30 -l 60). trimmed reads were mapped to the s. stercoralis reference genome (gca_000947215.1) and the small subunit ribosomal rna (ssu rrna; af279916) using bwa […]


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skewer in publications

 (38)
PMCID: 5897349
PMID: 29651122
DOI: 10.1038/s41598-018-24126-3

[…] deposited into european nucleotide archive (project accession no.: prjeb21189). sample metadata along with sample accession numbers are given in table . we demultiplexed resulting fastq files using skewer and assembled paired-end reads by pear. subsequently, using dada2 we eliminated sequences, where the expected number of sequencing errors was higher than one and performed denoising […]

PMCID: 5871668
PMID: 29619042
DOI: 10.3389/fgene.2018.00094

[…] in table . we performed quality control checks for all libraries with fastqc v. 0.10.1 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.) reads for strain cbs6556 were trimmed using skewer v. 0.2.2 (jiang et al., ) with parameters -q 20 -m pe -l 70. for blast analyses, de novo assemblies of each newly sequenced genome were made using spades 3.5.0 (bankevich et al., )., se, […]

PMCID: 5794922
PMID: 29391536
DOI: 10.1038/s41598-018-20372-7

[…] xt library generation. nextera xt libraries from bulks were pooled and sequenced together with the single-cell libraries., rna-seq reads were trimmed for nextera and illumina adapter sequences using skewer-v0.1.125. trimmed reads were mapped to a modified reference genome comprising the human genome homo sapiens grch37 (human_g1k_v37, available […]

PMCID: 5784092
PMID: 29367590
DOI: 10.1038/s41598-018-19430-x

[…] fastqc to check for overall quality of the data and used trimmomatic vers. 35 to trim adaptors (see table  for adaptor sequences), crop base 249, and remove reads shorter than 100 bp. we also used skewer vers. 0.1.127 to remove adaptor fragments., using as starting material a mixture of muscle, liver and brain, we prepared two size selected mate-pair libraries following illumina’s nextera mate […]

PMCID: 5802560
PMID: 29317592
DOI: 10.1038/s41398-017-0022-5

[…] version 1.8.2., the university of wisconsin-madison biotechnology center performed data analysis on the 16s rrna sequencing. briefly, sequencing reads were adapter and quality trimmed using the skewer trimming program. flash was used to merge paired end reads into amplicon sequences. merged amplicons were then quality filtered. qiime analysis used an open-reference operational taxonomic […]


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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 !