Software and supporting material for "SMAP: a streamlined methylation pipelinefor bisulphite sequencing".

Dataset type: Workflow, Software, Epigenomic
Data released on June 30, 2015

Gao S; Zou D; Mao L; Zhou Q; Jia W; Huang Y; Zhao S; Chen G; Wu S; Li D; Xia F; Chen H; Chen M; Orntoft TF; Bolund L; Sorensen KD (2015): Software and supporting material for "SMAP: a streamlined methylation pipelinefor bisulphite sequencing". GigaScience Database. http://dx.doi.org/10.5524/100143

DOI10.5524/100143

DNA methylation plays important roles in regulating gene expression and cellular specification. Reduced representation bisulfite sequencing (RRBS) has become prevailing in methylation studies due to its cost-effectiveness and single-base resolution. The rapid accumulation of RRBS data demands ingeniously and practically designed analytical tools. To streamline the data processing of DNA methylation in multiple RRBS samples, we present a flexible pipeline named SMAP, whose features include: 1) it handles single- and/or paired-end (SE/PE) diverse bisulfite sequencing data with reduced false positive rate in differentially methylated regions; 2) it detects allele-specific methylation events with improved algorithm; 3) it has a build-in pipeline for novel single nucleotide polymorphisms (SNP) detection; 4) it supports user-defined multiple restriction enzymes; 5) it basically conducts a one-step operation in all methylation analyses. SMAP is a modular pipeline implemented in Perl that calls software components written in C/C++, Perl, R and Java. Required input files for SMAP include BS or RRBS data in FASTQ format and a user-defined configuration file including all settings of the pipeline

Additional details

Read the peer-reviewed publication(s):

Gao, S., Zou, D., Mao, L., Zhou, Q., Jia, W., Huang, Y., … Sørensen, K. D. (2015). SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing. GigaScience, 4(1). doi:10.1186/s13742-015-0070-9

Additional information:

https://github.com/gaosjlucky/SMAPdigger

Accessions (data included in GigaDB):

SRA: SRA269060





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
K1_MB9606HumanhumanHomo sapiens Patient ID:K1
Tissue:brain(UBERON:0000955)
Is tumor:yes
...
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K1_MVC9606HumanhumanHomo sapiens Patient ID:K1
Tissue:blood vessel(UBERON:0001981)
Is tumor:yes
...
+
K1_normal9606HumanhumanHomo sapiens Patient ID:K1
Tissue:Kidney(UBERON:0002113)
Is tumor:no
...
+
K1_pRCC9606HumanhumanHomo sapiens Patient ID:K1
Tissue:Kidney(UBERON:0002113)
Is tumor:yes
...
+
Displaying 1-4 of 4 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
K1_normalMethylome dataFASTQ1.84 GB2015-05-20
K1_normalMethylome dataFASTQ1.6 GB2015-05-20
K1_normalMethylome dataFASTQ1.73 GB2015-05-20
K1_normalMethylome dataFASTQ1.47 GB2015-05-20
K1_MBMethylome dataFASTQ1.73 GB2015-05-20
K1_MBMethylome dataFASTQ1.52 GB2015-05-20
K1_MBMethylome dataFASTQ1.57 GB2015-05-20
K1_MBMethylome dataFASTQ1.33 GB2015-05-20
K1_pRCCMethylome dataFASTQ1.03 GB2015-05-20
K1_pRCCMethylome dataFASTQ874.29 MB2015-05-20
Displaying 1-10 of 57 File(s).
Funding body Awardee Award ID Comments
Danish Strategic Research Council
The Danish Cancer Society
National Natural Science Foundation of China 61202127
Ministry of Education of the People's Republic of China 60911062
Date Action
July 2, 2015 Dataset publish
October 27, 2015 File Normal.pe50.1.fq updated
October 27, 2015 File hg19.fa updated
October 27, 2015 File hg19.fa updated
October 27, 2015 File hg19.fa updated
October 27, 2015 File hg19.fa updated
October 27, 2015 File hg19.fa updated
October 27, 2015 File hg19.fa updated
October 27, 2015 File data.tar.gz updated
October 28, 2015 File RRBS_Kit_Addon.tar.gz updated
November 5, 2015 File hg19.fa updated
November 5, 2015 File hg19.fa updated