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seqyclean specifications


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




No version available



  • person_outline Ilya Zhbannikov

seqyclean citations


Contrasting the Genetic Patterns of Microbial Communities in Soda Lakes with and without Cyanobacterial Bloom

Front Microbiol
PMCID: 5827094
PMID: 29520256
DOI: 10.3389/fmicb.2018.00244
call_split See protocol

[…] 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 in the […]


Genome wide characterization of genetic variants and putative regions under selection in meat and egg type chicken lines

BMC Genomics
PMCID: 5785814
PMID: 29370772
DOI: 10.1186/s12864-018-4444-0

[…] 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 B […]


Polymorphic duplicate genes and persistent non coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders

BMC Genomics
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 “” 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 for an add […]


Rapid neo sex chromosome evolution and incipient speciation in a major forest pest

Nat Commun
PMCID: 5693900
PMID: 29150608
DOI: 10.1038/s41467-017-01761-4

[…] from the male and female genome builds (accessions SRX180259, SRX180261, and SRX180262) to identify putative X, Y and autosomal scaffolds using relative sequencing coverage between the sexes. We used SeqyClean version 1.8.10 to quality filter, adapter trim, and screen for common Acinetobacter contaminants (accessions CP000521, ACPN01000000). Filtered reads were then mapped to the reference male ge […]


Impact of hormonal modulation at proestrus on ovarian responses and uterine gene expression of suckled anestrous beef cows

PMCID: 5664832
PMID: 29118976
DOI: 10.1186/s40104-017-0211-3
call_split See protocol

[…] Raw sequences were trimmed for adaptors and low quality using SeqyClean v1.3.12. ( using 26 Phred quality parameter for maximum average error and a fasta file with contaminant sequences from the Univec database (https://www.ncb […]


Characterization of Four Multidrug Resistance Plasmids Captured from the Sediments of an Urban Coastal Wetland

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

[…] na, 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) were […]


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