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