BS Seeker protocols

BS Seeker specifications

Information


Unique identifier OMICS_00578
Name BS Seeker
Alternative names BS-Seeker2, BS-Seeker3
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Sequenced data
Input format FASTA, FASTAQ, qseq, pure sequence (one-line one-sequence)
Output data Alignment result, DNA methylomes
Output format SAM/BAM, tab-delimited text, wig
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages Python
License MIT License
Computer skills Advanced
Version 2.1.2
Stability Beta
Requirements PySam, Bowtie/Bowtie2
Source code URL https://codeload.github.com/BSSeeker/BSseeker2/tar.gz/v2.1.2Beta
Maintained Yes

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Versioning


Add your version

Documentation


Maintainers


  • person_outline Matteo Pellegrini <>
  • person_outline Pao-Yang Chen <>
  • person_outline BS-Seeker2 <>

Information


Unique identifier OMICS_00578
Name BS Seeker
Alternative names BS-Seeker2, BS-Seeker3
Interface Web user interface
Restrictions to use None
Input format FASTA, FASTAQ, qseq, pure sequence (one-line one-sequence)
Output format SAM/BAM, tab-delimited text, wig
Programming languages Python
Computer skills Basic
Version 2.0.9
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Matteo Pellegrini <>
  • person_outline Pao-Yang Chen <>
  • person_outline BS-Seeker2 <>

Publications for BS Seeker

BS Seeker IN pipeline

2017
PMCID: 5788436
PMID: 28925810
DOI: 10.1080/15592294.2017.1376151

[…] and 12 samples were pooled per lane on the hiseq4000., for all samples raw fastq files were filtered and trimmed using trimmomatic.47 for wgbs, reads were aligned to the human genome (hg38) using bs-seeker2.48 dmrs were called using the r packages dss and bsseq and custom r commands.49,50 for rna-seq, reads were aligned to hg38 using tophat2.51 differentially expressed genes were calculated […]

BS Seeker institution(s)
Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing, China; Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, CA, USA; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA; Zymo Research Corp, Irvine, CA, USA; Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, Richardson, TX, USA; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan; Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
BS Seeker funding source(s)
Supported by the Institute of Genomics and Proteomics at UCLA, NSFC (91019016) and NBRPC (2012CB316503) and the China Scholarship Council.

BS Seeker review

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Weilong Guo

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Desktop
BS-Seeker2 is well maintained. It has multiple advantages, such as defining CGmap/ATCGmap formats, support RRBS libraries, and using in silico method to remove reads failed in BS-conversion.