BS Seeker protocols

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BS Seeker statistics

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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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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 pipelines

 (4)
2017
PMCID: 5522596
PMID: 28732548
DOI: 10.1186/s13059-017-1273-4

[…] per-base sequence qualities and reads shorter than 70 bases after trimming were removed using prinseq []. the read mapping to the reference genome and methylation base calling was performed using bs-seeker2 []. the lumrs were identified for both cg and chg data using methylseekr []. the threshold for percent methylation for the low methylated regions (lmrs) was set to 20%. methylseekr [] […]

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. for wgbs, reads were aligned to the human genome (hg38) using bs-seeker2. dmrs were called using the r packages dss and bsseq and custom r commands. for rna-seq, reads were aligned to hg38 using tophat2. differentially expressed genes were calculated using […]

2016
PMCID: 4855439
PMID: 27146629
DOI: 10.1186/s12864-016-2653-y

[…] producing a cleaned set of 334.8 m and 274.8 m paired end reads for brain and blood, respectively. these reads were aligned to the great tit reference genome [] using bs-seeker v2.0.6 [] with bowtie2 v2.1.0 using the local alignment mode []. in total, 95,79 and 98.04 % of the genome was covered with an average depth of 31.89x (52 % mapping rate) and 33.04x (64 % […]

2016
PMCID: 4855439
PMID: 27146629
DOI: 10.1186/s12864-016-2653-y

[…] to a total read length of 100 bp from one end (single-end sequencing) of the molecules. raw reads were trimmed using trim_galore v 0.4.1 and aligned to the great tit reference genome [] using bs-seeker v2.0.10 in --rrbs mode [] with bowtie2 v2.2.7 using the local alignment mode []. this resulted in a mappability of 75.43 and 75.94 %. methylation levels were determined using […]


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BS Seeker in publications

 (55)
PMCID: 5917015
PMID: 29725341
DOI: 10.3389/fpls.2018.00497

[…] by hannon lab to remove bias and get higher quality reads. as reference the z. mays genome (agpv3) provided by the maize genetics and genomics database () was used. the alignment was done by bs-seeker2, which produces a reduced representation genome from the reference genome to increase mappability and accuracy of the alignment by virtually cutting with mspi and size-selecting […]

PMCID: 5890265
PMID: 29632298
DOI: 10.1038/s41467-018-03724-9

[…] reads were then quality trimmed and adaptors were removed using bbduk2 included in bbmap (mink = 3 qtrim = r trimq = 10 minlength = 20). for the mapping to the reference genomes, we used bs-seeker2, relying on bowtie2 end-to-end alignments, and using sambamba rmdup to eliminate pcr duplicates. methylation calls were genotype corrected using read data from bs-seeker2 atcgmap output […]

PMCID: 5747346
PMID: 29333247
DOI: 10.5256/f1000research.14317.r28483

[…] for all the mapped reads. a number of software tools have been developed for the purposes of read mapping and methylation calling of bs-seq data. popular ones include bismark , methylcoder , brat , bs-seeker and bsmap . most of the software tools rely on existing short read aligners, such as bowtie ., typical downstream dna methylation studies often involve finding differentially methylated […]

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. for wgbs, reads were aligned to the human genome (hg38) using bs-seeker2. dmrs were called using the r packages dss and bsseq and custom r commands. for rna-seq, reads were aligned to hg38 using tophat2. differentially expressed genes were calculated using […]

PMCID: 5692608
PMID: 29078418
DOI: 10.1073/pnas.1716758114

[…] (). dna sequences were aligned to the soybean genome (version wm82.a1; https://www.soybase.org) () or arabidopsis genome (version tair10; https://www.arabidopsis.org/index.jsp) () using bs seeker software (), allowing up to two base mismatches. the sequencing depth for each cytosine in the reference genome was defined as the total number of detected cytosines (methylated c) […]


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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.