Bisulfite Sequencing Virus integration Finder

For directional libraries only. PBAT and indirectional libraries are NOT supported.

bwa-meth 0.10 depends on

• python 2.7+ (including python3)

  • toolshed library. can be installed with:
    • easy_install toolshed or
    • pip install toolshed

• samtools command on the $PATH (https://github.com/samtools/samtools)

• bwa mem from: https://github.com/lh3/bwa

• EMBOSS from: http://emboss.sourceforge.net/

Run pip install toolshed.

Run src/install.sh.

In case EMBOSS failed to install, you'll need to download the binary from above sites. And put water of EMBOSS in to ./bin. Or, just link water to ./bin.

Your bsIntegration/bin/ should be like this:

-rwxr-xr-x  398860 Feb 20 00:48 bwa
-rwxr-xr-x   21892 Sep  1 08:37 bwameth.py
-rwxr-xr-x   27040 Feb 20 01:14 water
-rwxr-xr-x  971772 Feb 20 00:48 samtools

./bsuit <command> <config_file>

./bsuit prepare prj.ini
./bsuit aln prj.ini
./bsuit grep prj.ini
./bsuit analyse prj.ini

mkdir sim90 && cd sim90 && ./simVirusInserts.pl GRCh38_no_alt_analysis_set.fna.gz X04615.fa.gz s90 && cd ..
mkdir sim50 && cd sim50 && ./simVirusInserts.pl GRCh38_no_alt_analysis_set.fna.gz X04615.fa.gz s50 50 ../sim90/s90.ini && cd ..

./bsuit prepare sim90/s90.ini

./bsuit aln sim90/s90.ini
./run/s90_aln.sh
./bsuit grep sim90/s90.ini
./bsuit analyse sim90/s90.ini

./bsuit aln sim50/s50.ini
./run/s50_aln.sh
./bsuit grep sim50/s50.ini
./bsuit analyse sim50/s50.ini

• Human: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
• HBV: gi|59585|emb|X04615.1| Hepatitis B virus genome, subtype ayr

./simVirusInserts.pl GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz HBV.X04615.fa sim150 150

A gzipped file that contains FASTA format sequences for the following:

1. chromosomes from the GRCh38 Primary Assembly unit.
   Note: the two PAR regions on chrY have been hard-masked with Ns.
   The chromosome Y sequence provided therefore has the same coordinates as the GenBank sequence but it is not identical to the GenBank sequence. Similarly, duplicate copies of centromeric arrays and WGS on chromosomes 5, 14, 19, 21 & 22 have been hard-masked with Ns (locations of the unmasked copies are given below).
2. mitochondrial genome from the GRCh38 non-nuclear assembly unit.
3. unlocalized scaffolds from the GRCh38 Primary Assembly unit.
4. unplaced scaffolds from the GRCh38 Primary Assembly unit.
5. Epstein-Barr virus (EBV) sequence
   Note: The EBV sequence is not part of the genome assembly but is included in the analysis set as a sink for alignment of reads that are often present in sequencing samples.

[RefFiles]
HostRef=/share/HomoGRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
VirusRef=/share/work/bsvir/HBV.AJ507799.2.fa

[DataFiles]
780_T.1=/share/work/bsvir/F12HPCCCSZ0010_Upload/s00_C.bs_1.fq.gz
780_T.2=/share/work/bsvir/F12HPCCCSZ0010_Upload/s00_C.bs_2.fq.gz
s01_P.1=/share/work/bsvir/F12HPCCCSZ0010_Upload/s01_P.bs_1.fq.gz
s01_P.2=/share/work/bsvir/F12HPCCCSZ0010_Upload/s01_P.bs_2.fq.gz
;MultiLibExample.1=/test/Lib1/AAAA.1.fq.gz, /test/Lib2/AAAA.1.fq.gz, /test/Lib3/BBBB.1.fq.gz
;MultiLibExample.2=/test/Lib1/AAAA.2.fq.gz, /test/Lib2/AAAA_2.fq , /test/Lib3/BBBB.2.fq.gz
tSE_X.1=/share/work/bsvir/F12HPCCCSZ0010_Upload/s00_C.bs_1.fq.gz,/share/work/bsvir/F12HPCCCSZ0010_Upload/s01_P.bs_2.fq.gz

[InsertSizes]
780_T=200
780_T.SD=120
s01_P=200
s01_P.SD=30
;MultiLibExample=210
;MultiLibExample.SD=70
tSE_X=90
tSE_X.SD=1

[Output]
WorkDir=/share/work/bsvir/bsI
ProjectID=SZ2015

You'll need cmake and autoconf, automake and devel-libs, as well as gcc, g++ to compile all sources.

For Mac OS X, install Homebrew first. Then:

xcode-select --install
brew install autoconf automake cmake python
brew install --without-multilib gcc

To Build the binaries:

cd src
./download.sh
./install.sh

pip install toolshed

• For comment lines, use ; as the first character.

• RefFiles Section

  • HostRef is Host genome.
  • VirusRef is Virus sequence.

• DataFiles Section

  • Each Sample need an unique ID as SampleID. Use SampleID.1 and SampleID.2 to specify pair-end sequencing data.
  • For samples with multiple PE sets, join each file with comma and keep their order.

• InsertSizes Section

  • For each SampleID, use SampleID to specify average insert sizes. And use SampleID.SD to specify its standard deviation.

• Output Section

  • WorkDir is the output directory.
  • ProjectID is an unique ID for this analyse defined in the config_file.

BSuit is a suit to analyse xxx.

Chr	breakpoint	virus-start virus-end virusstrand	how-many-reads-support cluster-name
Chr1	3000	200	300	+/-	20 cluster1

clustername contig-number chrpoint virus-integration
cluster1	contig1	chr1:3000	virus:+:200-300
cluster1	contig2	chr2:4000	viurs:-:300-400

Compare with ViralFusionSeq [VFS] and VirusFinder 2 on normal WGS data.

• Bismark 0.18.1

• SVDetect r0.8b

• ViralFusionSeq and Virus-Clip

• VirusSeq, which uses MOSAIK aligner.

• VirusFinder 2 (VERSE)

• Vy-PER

• seeksv

• BS-Seeker2

• Sherman

  • 模拟时甲基化率设为800.

* for virus-infected reads
# for integration infomation