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
orpip 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:
- 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). - mitochondrial genome from the GRCh38 non-nuclear assembly unit.
- unlocalized scaffolds from the GRCh38 Primary Assembly unit.
- unplaced scaffolds from the GRCh38 Primary Assembly unit.
- 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
SectionHostRef
is Host genome.VirusRef
is Virus sequence.
-
DataFiles
Section- Each Sample need an unique ID as SampleID. Use
SampleID.1
andSampleID.2
to specify pair-end sequencing data. - For samples with multiple PE sets, join each file with comma and keep their order.
- Each Sample need an unique ID as SampleID. Use
-
InsertSizes
Section- For each
SampleID
, useSampleID
to specify average insert sizes. And useSampleID.SD
to specify its standard deviation.
- For each
-
Output
SectionWorkDir
is the output directory.ProjectID
is an unique ID for this analyse defined in theconfig_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.
-
- 模拟时甲基化率设为800.
Tool | Sequencing Type | Programme Language | 1st Aligenment * | Assembler | 2nd Aligenment # | Epub Date |
---|---|---|---|---|---|---|
VirusSeq | RNA-Seq, WGS | Perl | MOSAIK to Human | MOSAIK to Virus | MOSAIK to Hybrid | 2012 Nov 08 |
ViralFusionSeq | RNA-Seq, WGS | Perl | BWA-SW to Human | cap3, SSAKE | Blastall to Virus | 2013 Jan 12 |
VERSE(VirusFinder2) | WGS, RNA-Seq | Perl | Bowtie2 to Human, BLAT to Virus, BLASTN to Virus | Trinity | BWA-SW to Hybrid, SVDetect,CREST | 2015 Jan 20 |
Virus-Clip | RNA-seq | Perl | BWA-MEM to Virus | Virus-Clip | BLASTN to Human | 2015 May 19 |
Vy-PER | WGS, RNA-Seq | Python2 | BWA-SW to Human | Vy-PER | BLAT to Virus | 2015 Jul 13 |
seeksv | WGS | C++ | BWA to Hybrid | seeksv | seeksv to Hybrid | 2016 Sep 14 |
BSVF | WGBS, WGS | Perl,C,C++ | BWA-MEM to Hybrid | BSVF | water(EMBOSS) to Hybrid | N/A |
* for virus-infected reads
# for integration infomation