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

bismark_genome_preparation needs to be run to prepare the genome of interest for bisulfite alignments. You need to specify a directory containing the genome you want to align your reads against (please be aware that the bismark_genome_preparation script currently expects FastA files in this folder (with either .fa or .fasta extension, single or multiple sequence entries per file). Bismark will create two individual folders within this directory, one for a C->T converted genome and the other one for the G->A converted genome. After creating C->T and G->A versions of the genome they will be indexed in parallel using the indexer bowtie-build (or bowtie2-build). Once both C->T and G->A genome indices have been created you do not need to use the genome preparation script again

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. Its 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