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BS Seeker

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Alternative name: BS-Seeker2

Allows to map the bisulfite-treated short reads. BS Seeker is a bisulfite sequencing (BS) alignment tool that performs genome indexing, read alignment and DNA methylation levels calling for each cytosine. The software was improved utilizing multiple short-read mapping aligners, supporting gapped mapping and local alignment and building special indexes for handling reduced represented bisulfite sequencing (RRBS) data.

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1 user review

1 user review

Weilong Guo's avatar image Weilong Guo's country flag

Weilong Guo

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.

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BS Seeker classification

BS Seeker specifications

Software type:
Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTA, FASTAQ, qseq, pure sequence (one-line one-sequence)
Output format:
SAM/BAM, tab-delimited text, wig
Operating system:
Unix/Linux, Mac OS
License:
MIT License
Version:
2.1.2
Requirements:
PySam, Bowtie/Bowtie2
Interface:
Command line interface
Input data:
Sequenced data
Output data:
Alignment result, DNA methylomes
Biological technology:
Illumina
Programming languages:
Python
Computer skills:
Advanced
Stability:
Beta
Maintained:
Yes

BS Seeker distribution

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No review has been posted.

BS Seeker forum

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No open topic.

BS Seeker classification

BS Seeker specifications

Interface:
Web user interface
Input format:
FASTA, FASTAQ, qseq, pure sequence (one-line one-sequence)
Programming languages:
Python
Version:
2.0.9
Maintained:
Yes
Restrictions to use:
None
Output format:
SAM/BAM, tab-delimited text, wig
Computer skills:
Basic
Stability:
Stable

BS Seeker support

Documentation

Maintainers

Credits

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Publications

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

Funding source(s)

Supported by the Institute of Genomics and Proteomics at UCLA, NSFC (91019016) and NBRPC (2012CB316503) and the China Scholarship Council.

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