Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria
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   Max F. Perutz Laboratories
   University of Vienna
   Medical University, Vienna

   Deep Metazoan Phylogeny
   MaBS group
   Max Perutz Library

Welcome to Bisulfite Sequencing Scorer (BiSS)


BiSS (Bisulfite Sequencing Scorer) is an analysis pipeline for the deep sequencing data after bisulfite conversion (BS-Seq).

Mapping procedure:

  • using banded Smith-Waterman local alignment algorithm
  • implemented in the Graphical Processing Unit based package NextGenMap.
  • special asymmetric scoring function
  • 3.5 letter hashing table.
  • Downstream analysis (methylation calling):

    We are currently maintaining the code and updating it. In the mean time we recommend to use Bis-SNP ( http://epigenome.usc.edu/publicationdata/bissnp2011/).

    Sorry for the inconvenience.

    Running instruction

  • Running: ngm -r reference_filename -q read_filename -t number_of_threads_used -o output_filename --bs-mapping
  • Running with paired-end data: ngm -1 read1_filename -2 read2_filename -r reference_filename -o output_filename -t number_of_threads_used --bs-mapping
  • Please also provide the read group information as this is required for Bis-SNP:
    --rg-sm RG header: Sample
    --rg-lb RG header: Library
    --rg-pl RG header: Platform
    --rg-ds RG header: Description
    --rg-dt RG header: Date
    --rg-pu RG header: Platform unit
    --rg-pi RG header: Median insert size
    --rg-pg RG header: Programs
    --rg-cn RG header: sequencing center
    --rg-fo RG header: Flow order
    --rg-ks RG header: Key sequence
  • You can use the following parameter to speed up the mapping: -s 0.8 --kmer-skip 4
  • Post processing: java -Xmx10g -jar BisSNP-0.82.2.jar -R reference_filename -I output_filename.bam -T BisulfiteGenotyper -vfn1 cpg.raw.vcf -vfn2 snp.raw.vcf -stand_call_conf 20 -stand_emit_conf 0 -mmq 30 -mbq 0
  • Availability:

    Latest version BiSS-on-NextGenMap:

    • Please read the User Manual carefully before using NextGenMap the first time or when you upgrade the new version! 
    • The current version of NextGenMap is currently only tested and released under Linux.


    We are always intrested in feedback on how we can improve NextGenMap. If you have any suggestions please do not hesitate to either leave a note in the issue section or to contact us directly:



    contact imprint .