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

Welcome to Bisulfite Sequencing Scorer (BiSS)


Introduction:

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.

    Contact:

    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:

    fritz.sedlazeck@univie.ac.at

    philipp.rescheneder@univie.ac.at


    Printable version of: http://www.cibiv.at/software/ngm/BiSS/index.shtml

    contact imprint .