Table 2 Comparison of existing software programs for bisulfite sequencing analysis (Adapted from [14])
Software | Programming Language and Implementation | Analysis Process | Visual Output | Input File | Output File | EHA | Epihaplotype Counts | Experiment Quality Check |
|---|---|---|---|---|---|---|---|---|
MethPat | Python, pip install, URL available to install files locally. | Summarises Bismark output. | Interactive HTML and summary text file of epihaplotype counts. Scalable PNG file. | Bismark methylation extractor output, user-defined BED format file. | HTML and tab delimited text file. | No | Yes | No, made by Bismark. |
Bismark | Command line, Python, requires bwa. | Performs alignment to bisulfite reference genome. | None, generates BAM files for visualisation with SeqMonk or IGV. | FASTQ file. | BAM and tab delimited text files. | No | No | Yes computes C to T conversion. |
BSPAT | Java/JSP web interface. | Visualization and summarization of Bismark output. | PNG file and UCSC Genome Browser file. | Bismark output, FASTQ files. | Text file summary, PNG and UCSC Genome Browser BED file. | No | Yes | No |
MPFE | R library, Bioconductor. | Calculates probabilities that epihaplotypes are true. | R image outputs. | Table of read counts from bisulfite sequencing data. | Derived statistics and plots. | No | Yes | Yes |
Methylation plotter | R library, shiny interactive web application. | Visualizes beta DNA methylation values. | Interactive webpage with setting options to adjust a static image of DNA methylation values for each sample. PNG and PDF output. | Text file containing matrix of sample vs beta value at each CpG of interest. | PDF and PNG image file. | No | No | No |
RnBeads | R library, Bioconductor. | Processes summary data from other software for visualization. | Interactive HTML and UCSC Genome browser track hub files. PNG files. | BED file | HTML summary | No | No | Yes |
coMET | R library, Webserver for analysis. | For EWAS studies. Analyses derived matrix files. | Image files of plots with genomic locations. | Text matrix files | Image files | No | No | No |
AmpliMethProfiler | Python, BLAST and QIIME | Filtering and de-multiplexing of the sequence, generation of the methylation status and EpiHaplotype composition analysis. | HTML plots and summary text file. An heatmap in PDF format. An Alpha and a Beta diversity plot in HTML and PDF format. | A fasta directory with all fasta for each sample. A file containing the reads from the sequencer. A metaFile containing information about the samples. | Filtered Fasta file. Blast aligned sequences in XML and TXT format. Summary and quality statistics for region. CpG methylation profile matrix. BIOM file with number of occurrences. | Yes | Yes | Yes, quality statistic for each analyzed region. |