seqyclean pipeline

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



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  • person_outline Ilya Zhbannikov <>

seqyclean IN pipelines

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

[…] the male and female genome builds29 (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 […]

PMCID: 4727422
PMID: 26685325
DOI: 10.1194/jlr.M064808

[…] was extracted from approximately 1,000 nematodes using a qiagen dneasy kit. samples were sequenced using a miseq pe250 run with an expected coverage of ∼10× per sample. reads were then cleaned with seqyclean, mapped against the wbcel215.70 ( using bowtie 2 v2.1.0, and variants were called with the samtools package […]

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