seqyclean protocols

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seqyclean specifications

Information


Unique identifier OMICS_20624
Name seqyclean
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format SFF, FASTQ
Output format GZIP
Biological technology Illumina, Roche
Operating system Unix/Linux, Mac OS
Programming languages C, C++, Shell (Bash)
License MIT License
Computer skills Advanced
Version 1.9.11
Stability Stable
Maintained Yes

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  • person_outline Ilya Zhbannikov <>

seqyclean in pipelines

 (15)
2018
PMCID: 5785814
PMID: 29370772
DOI: 10.1186/s12864-018-4444-0

[…] on library preparation and sequencing can be obtained from moreira et al. []., first, the quality of the sequencing reads was checked with fastqc tool []. read quality trimming was performed using seqyclean tool (v.1.3.12) [] to select reads with average phred score quality ≥ 24 and minimum length of 65 bp. the reads were aligned against the gallus_gallus-4.0 chicken reference genome [] using […]

2018
PMCID: 5827094
PMID: 29520256
DOI: 10.3389/fmicb.2018.00244

[…] v3 (600 cycles) (illumina)., for the shotgun metagenomic dataset, overlapping reads were paired using pear 0.9.5 () and filtered for quality with phred > 30, and a length longer than 80 nt using seqyclean 1.9.8. the reads were annotated by blastx against the ncbi-nr database (november 2016) using diamond (). retrieved annotations were later analyzed using megan6 (). the data presented […]

2018
PMCID: 5902700
PMID: 29692800
DOI: 10.3389/fgene.2018.00120

[…] 0.10.1) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). all reads were filtered for phred quality (qs) 23 (sequence inside) and 30 (sequence edges) and minimum length of 65 bp using the seqyclean software (v.1.9.9) (https://github.com/ibest/seqyclean). the same package was also used to remove contaminant sequences (primers and vectors) using the univec database […]

2017
PMCID: 5480813
PMID: 28664146
DOI: 10.1016/j.gdata.2017.06.004

[…] and validated using the bioanalyzer. paired-end sequencing of 101 bp reads was performed using the illumina hiseq 2000 (ampulla samples) and illumina hiseq 2500 (isthmus samples) platforms. using seqyclean v1.3.12. (https://bitbucket.org/izhbannikov/seqyclean/get/stable.zip) the quality filtering was performed. in order to generate the mapping file, accepted reads were mapped with tophat […]

2017
PMCID: 5664832
PMID: 29118976
DOI: 10.1186/s40104-017-0211-3

[…] funcional aplicado a agropecuária e agroenergia at the university of são paulo using a hiscansq sequencer (illumina, san diego, ca)., raw sequences were trimmed for adaptors and low quality using seqyclean v1.3.12. (https://github.com/ibest/seqyclean) using 26 phred quality parameter for maximum average error and a fasta file with contaminant sequences from the univec database […]


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seqyclean in publications

 (23)
PMCID: 5902700
PMID: 29692800
DOI: 10.3389/fgene.2018.00120

[…] 0.10.1) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). all reads were filtered for phred quality (qs) 23 (sequence inside) and 30 (sequence edges) and minimum length of 65 bp using the seqyclean software (v.1.9.9) (https://github.com/ibest/seqyclean). the same package was also used to remove contaminant sequences (primers and vectors) using the univec database […]

PMCID: 5745709
PMID: 29281973
DOI: 10.1186/s12864-017-4358-2

[…] genbank sra (prjna407969). we screened all shotgun reads to eliminate sequencing adapters, identify and remove contaminants, and trim reads based on quality scores using the bioinformatics pipeline “seqyclean.py” provided by the ibest computational resources core. we assembled the remaining shotgun reads into contigs using newbler v.2.6. we also included published shotgun sequence data […]

PMCID: 5644112
PMID: 29037161
DOI: 10.1186/s12864-017-4170-z

[…] to assembly, reads from all replicates were merged into a single dataset and the resulting fastq files (illumina) were filtered to remove low-quality bases (score < 30) and adapters, using the seqyclean pipeline (https://github.com/ibest/seqyclean). the remaining data were normalized by a single-pass digital normalization using the “normalize_by_kmer_coverage” procedure of the trinity […]

PMCID: 5641379
PMID: 29067005
DOI: 10.3389/fmicb.2017.01922

[…] san diego, ca, united states). prior to analysis, duplicate read pairs were removed using a custom python script. sequencing adapters and low-quality bases were removed using the software package seqyclean. all remaining reads were mapped to the chromosome of either e. coli o157:h7 (ba000007.2) or p. putida kt2442 (nc_002947.3) using bowtie2. the unused reads (i.e., non-chromosomal reads) […]


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