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By Krueger F., Andrews S.R., Last update 1494699000
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deduplicate_bismark description

deduplicate_bismark removes alignments to the same position in the genome which can arise by e.g. PCR amplification Paired-end alignments are considered a duplicate if both partner reasd start and end at the exact same position

Parent program: bismark

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: (1) bisulfite mapping and methylation calling in one single step; (2) Supports single-end and paired-end read alignment; (3) Supports ungapped and gapped alignments (4) Alignment seed length, number of mismatches etc. are adjustable (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context