| Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. It's main features are: - Bisulfite mapping and methylation calling in one single step - Supports single-end and paired-end read alignments - Supports ungapped and gapped alignments - Alignment seed length, number of mismatches etc. are adjustable - Output discriminates between cytosine methylation in CpG, CHG and CHH context http://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/bismark
| Repository package_samtools_0_1_19 revision c9bd782f5342 owned by iuc |
| Name | Version | Type | |
|---|---|---|---|
| bowtie | 0.12.8 | package | |
| bowtie2 | 2.1.0 | package | |
| samtools | 0.1.19 | package | |
| SCRIPT_PATH | set_environment | ||
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Reports on methylation status of reads mapped by Bismark | 0.10.2 | any | |
| bisulfite mapper (bowtie) | 0.10.2 | any | |
| bisulfite mapper (bowtie2) | 0.10.2 | any | |