perl/bsvf/README.md

   1 # BSVF
   2 [Bisulfite Sequencing Virus integration Finder](https://github.com/BGI-SZ/BSVF)
   3
   4 Repo URL: <https://github.com/BGI-SZ/BSVF>
   5
   6 ## Attention
   7
   8 For directional libraries only. PBAT and indirectional libraries are _NOT_ supported.
   9
  10 ## Dependencies
  11
  12 [bwa-meth 0.10](https://github.com/brentp/bwa-meth/tree/0a2f9fc7c3fd3c99c4212941c94be73c9c865bb1) depends on
  13
  14  + python 2.7+ (including python3)
  15    - `toolshed` library. can be installed with:
  16       * `easy_install toolshed` or
  17       * `pip install toolshed`
  18
  19  + samtools command on the `$PATH` (https://github.com/samtools/samtools)
  20
  21  + bwa mem from: https://github.com/lh3/bwa
  22
  23  + EMBOSS from: http://emboss.sourceforge.net/
  24
  25 ## Install
  26
  27 ### [Nerdy](https://thelinuxexperiment.com/?s=nerdy)
  28
  29 Since the project leader wants to include all relevant tools here, even if they are already provided by main Linux distributions.
  30
  31 For problems on compiling `EMBOSS`, `BWA` or `SAMTOOLS`/`HTSLIB`, please ask the original programmer.
  32
  33 ````bash
  34 pip install toolshed
  35 apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev
  36 #yum install autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel
  37 git clone https://github.com/BGI-SZ/BSVF.git
  38 cd BSVF
  39 git submodule init
  40 git submodule update
  41 src/install.sh
  42 ````
  43
  44 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`.
  45
  46 Your `BSVF/bin/` should be like this:
  47
  48 ````bash
  49 -rwxr-xr-x  398860 Feb 20 00:48 bwa
  50 -rwxr-xr-x   21892 Sep  1 08:37 bwameth.py
  51 -rwxr-xr-x   27040 Feb 20 01:14 water
  52 -rwxr-xr-x  971772 Feb 20 00:48 samtools
  53 ````
  54
  55 ### Debian
  56
  57 ````bash
  58 apt install libbam-dev libhts-dev python3-pip emboss bwa samtools
  59 pip install toolshed
  60 git clone https://github.com/BGI-SZ/BSVF.git
  61 cd BSVF/src/analyser
  62 make
  63 cd BSVF/bin
  64 [symbolic link `bwa`, `samtools` and `water` from /usr/bin/ or so]
  65 ````
  66
  67 ### Homebrew/Linuxbrew
  68
  69 ````bash
  70 brew tap Ensembl/homebrew-external
  71 brew install emboss bwa samtools python
  72 pip install toolshed
  73
  74 ln -s `which bwa` ./bin/
  75 ln -s `which samtools` ./bin/
  76 ln -s `which water` ./bin/
  77
  78 brew install gcc
  79 cd ./src/analyser/
  80 make
  81 cp -av analyser/bsanalyser ../../bin/
  82 cd ../../bin/
  83 ls -l
  84 ````
  85
  86 ## Citation
  87
  88 Gao, S., Hu, X., Xu, F., Gao, C., Xiong, K., Zhao, X., … Pedersen, C. N. S. (2018). BS-virus-finder: virus integration calling using bisulfite sequencing data. GigaScience, 7(1), 1–7. <https://doi.org/10.1093/gigascience/gix123>
  89
  90 ## Usage
  91
  92 ```
  93 ./bsuit <command> <config_file>
  94
  95 ./bsuit prepare prj.ini
  96 ./bsuit aln prj.ini
  97 ./bsuit grep prj.ini
  98 ./bsuit analyse prj.ini
  99 ```
 100
 101 ![a Logo](https://raw.githubusercontent.com/BGI-SZ/BSVF/master/logo/BSVFlogo.png)
 102
 103 ## Test Run
 104
 105 ```
 106 mkdir sim90 && cd sim90 && ./simVirusInserts.pl GRCh38_no_alt_analysis_set.fna.gz X04615.fa.gz s90 && cd ..
 107 mkdir sim50 && cd sim50 && ./simVirusInserts.pl GRCh38_no_alt_analysis_set.fna.gz X04615.fa.gz s50 50 ../sim90/s90.ini && cd ..
 108
 109 ./bsuit prepare sim90/s90.ini
 110
 111 ./bsuit aln sim90/s90.ini
 112 ./run/s90_aln.sh
 113 ./bsuit grep sim90/s90.ini
 114 ./bsuit analyse sim90/s90.ini
 115
 116 ./bsuit aln sim50/s50.ini
 117 ./run/s50_aln.sh
 118 ./bsuit grep sim50/s50.ini
 119 ./bsuit analyse sim50/s50.ini
 120 ```
 121
 122 ## Reference Files
 123
 124  * 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>
 125  * HBV: [gi|59585|emb|X04615.1| Hepatitis B virus genome, subtype ayr](http://www.ncbi.nlm.nih.gov/nuccore/X04615.1?report=GenBank)
 126
 127 ## Simulation
 128
 129     ./simVirusInserts.pl GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz HBV.X04615.fa sim150 150
 130
 131 ### GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
 132
 133 A gzipped file that contains FASTA format sequences for the [following](ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/README_analysis_sets.txt):
 134
 135 1. chromosomes from the GRCh38 Primary Assembly unit.
 136    Note: the two PAR regions on chrY have been hard-masked with Ns.
 137    The chromosome Y sequence provided therefore has the same
 138    coordinates as the GenBank sequence but it is not identical to the
 139    GenBank sequence. Similarly, duplicate copies of centromeric arrays
 140    and WGS on chromosomes 5, 14, 19, 21 & 22 have been hard-masked
 141    with Ns (locations of the unmasked copies are given below).
 142 2. mitochondrial genome from the GRCh38 non-nuclear assembly unit.
 143 3. unlocalized scaffolds from the GRCh38 Primary Assembly unit.
 144 4. unplaced scaffolds from the GRCh38 Primary Assembly unit.
 145 5. Epstein-Barr virus (EBV) sequence
 146    Note: The EBV sequence is not part of the genome assembly but is
 147    included in the analysis set as a sink for alignment of reads that
 148    are often present in sequencing samples.
 149
 150 ## Format of `config_file`
 151
 152 ### An example
 153
 154 ```ini
 155 [RefFiles]
 156 HostRef=/share/HomoGRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz
 157 VirusRef=/share/work/bsvir/HBV.AJ507799.2.fa
 158
 159 [DataFiles]
 160 780_T.1=/share/work/bsvir/F12HPCCCSZ0010_Upload/s00_C.bs_1.fq.gz
 161 780_T.2=/share/work/bsvir/F12HPCCCSZ0010_Upload/s00_C.bs_2.fq.gz
 162 s01_P.1=/share/work/bsvir/F12HPCCCSZ0010_Upload/s01_P.bs_1.fq.gz
 163 s01_P.2=/share/work/bsvir/F12HPCCCSZ0010_Upload/s01_P.bs_2.fq.gz
 164 ;MultiLibExample.1=/test/Lib1/AAAA.1.fq.gz, /test/Lib2/AAAA.1.fq.gz, /test/Lib3/BBBB.1.fq.gz
 165 ;MultiLibExample.2=/test/Lib1/AAAA.2.fq.gz, /test/Lib2/AAAA_2.fq , /test/Lib3/BBBB.2.fq.gz
 166 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
 167
 168 [InsertSizes]
 169 780_T=200
 170 780_T.SD=120
 171 s01_P=200
 172 s01_P.SD=30
 173 ;MultiLibExample=210
 174 ;MultiLibExample.SD=70
 175 tSE_X=90
 176 tSE_X.SD=1
 177
 178 [Output]
 179 WorkDir=/share/work/bsvir/bsI
 180 ProjectID=SZ2015
 181
 182 [Parameters]
 183 Aligner=bwa-meth
 184 MinVirusLength=20
 185 ```
 186
 187 ## Build
 188
 189 You'll need `cmake` and `autoconf, automake` and devel-libs, as well as `gcc, g++` to compile all sources.
 190
 191 For Mac OS X, install [Homebrew](http://brew.sh/) first. Then:
 192 ```bash
 193 xcode-select --install
 194 brew install autoconf automake cmake python
 195 brew install --without-multilib gcc
 196 ````
 197
 198 To Build the binaries:
 199 ```bash
 200 cd src
 201 ./download.sh
 202 ./install.sh
 203
 204 pip install toolshed
 205 ```
 206
 207 ### Details
 208
 209  + For comment lines, use `;` as the first character.
 210
 211  + `RefFiles` Section
 212    - `HostRef` is **Host genome**.
 213    - `VirusRef` is **Virus sequence**.
 214
 215  + `DataFiles` Section
 216    - Each *Sample* need an **unique ID** as *SampleID*. Use `SampleID.1` and `SampleID.2` to specify pair-end sequencing data.
 217    - For samples with multiple PE sets, join each file with *comma* and keep their order.
 218
 219  + `InsertSizes` Section
 220    - For each `SampleID`, use `SampleID` to specify average insert sizes. And use `SampleID.SD` to specify its standard deviation.
 221
 222  + `Output` Section
 223    - `WorkDir` is the output directory.
 224    - `ProjectID` is an **unique ID** for this analyse defined in the `config_file`.
 225
 226 ## Description
 227
 228 **BSuit** is a suit to analyse xxx.
 229
 230 ### Formats
 231
 232 #### 病毒整合结果文件
 233
 234 ````
 235 Chr     breakpoint      virus-start virus-end virusstrand       how-many-reads-support cluster-name
 236 Chr1    3000    200     300     +/-     20 cluster1
 237 ````
 238
 239 #### 中间contig信息文件
 240
 241 ````
 242 clustername contig-number chrpoint virus-integration
 243 cluster1        contig1 chr1:3000       virus:+:200-300
 244 cluster1        contig2 chr2:4000       viurs:-:300-400
 245 ````
 246
 247 ## ToDo
 248
 249 Compare with [ViralFusionSeq [VFS]](https://sourceforge.net/projects/viralfusionseq/) and [VirusFinder 2](https://bioinfo.uth.edu/VirusFinder/) on normal WGS data.
 250
 251 ## See also
 252
 253 * [Bismark](https://www.bioinformatics.babraham.ac.uk/projects/bismark/) [0.18.1](https://github.com/FelixKrueger/Bismark/releases)
 254 * [SVDetect](https://sourceforge.net/projects/svdetect/) [r0.8b](https://sourceforge.net/projects/svdetect/files/SVDetect/0.80/)
 255 * [ViralFusionSeq](https://sourceforge.net/projects/viralfusionseq/) and [Virus-Clip](http://web.hku.hk/~dwhho/Virus-Clip.zip)
 256 * [VirusSeq](http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html), which uses [MOSAIK](https://github.com/wanpinglee/MOSAIK) aligner.
 257 * [VirusFinder 2 (VERSE)](https://bioinfo.uth.edu/VirusFinder/)
 258 * [Vy-PER](http://www.ikmb.uni-kiel.de/vy-per/)
 259 * [seeksv](https://github.com/qiukunlong/seeksv)
 260 * [BS-Seeker2](https://github.com/BSSeeker/BSseeker2)
 261
 262 * [Sherman](https://www.bioinformatics.babraham.ac.uk/projects/sherman/)
 263   * 模拟时甲基化率设为800.
 264
 265 | Tool | Sequencing Type | Programme Language | 1st Aligenment * | Assembler | 2nd Aligenment # | Epub Date |
 266 |:-----|:---------------:|:------------------:|:-----:|:-----:|:-----:|:-----:|
 267 |[VirusSeq](https://doi.org/10.1093/bioinformatics/bts665)|RNA-Seq, WGS|Perl|MOSAIK to Human|MOSAIK to Virus|MOSAIK to Hybrid|2012 Nov 08|
 268 |[ViralFusionSeq](https://doi.org/10.1093/bioinformatics/btt011)|RNA-Seq, WGS|Perl|BWA-SW to Human|cap3, SSAKE|Blastall to Virus|2013 Jan 12|
 269 |[VERSE(VirusFinder2)](https://doi.org/10.1186/s13073-015-0126-6)|WGS, RNA-Seq|Perl|Bowtie2 to Human, BLAT to Virus, BLASTN to Virus|Trinity|BWA-SW to Hybrid, SVDetect,CREST|2015 Jan 20|
 270 |[Virus-Clip](https://doi.org/10.18632/oncotarget.4187)|RNA-seq|Perl|BWA-MEM to Virus|Virus-Clip|BLASTN to Human|2015 May 19|
 271 |[Vy-PER](https://doi.org/10.1038/srep11534)|WGS, RNA-Seq|Python2|BWA-SW to Human|Vy-PER|BLAT to Virus|2015 Jul 13|
 272 |[seeksv](https://doi.org/10.1093/bioinformatics/btw591)|WGS|C++|BWA to Hybrid|seeksv|seeksv to Hybrid|2016 Sep 14|
 273 |BSVF|WGBS, WGS|Perl,C,C++|BWA-MEM to Hybrid|BSVF|water(EMBOSS) to Hybrid| N/A |
 274
 275 \* for virus-infected reads
 276 \# for integration infomation
 277
 278 ## One More Things
 279
 280 To extract relevant PE reads within 500 bp range from final result, *BS.analyse* for example.
 281
 282 ```bash
 283 perl -lane '$a=$F[2]-501;$b=$F[2]+501;print join("\t",$F[1],$a,$b)' ../W2BS_analyse/BS.analyse >zones.bed
 284 vi zones.bed # To remove the first head line
 285 # sort BS.bam to BS.sort.bam and index it.
 286 samtools view -L zones.bed BS.sort.bam > zones.sam
 287 awk '{print $1}' zones.sam | sort | uniq > zones.ids
 288 #samtools view BS.bam | grep -F -f zones.ids >zones.PE.sam
 289 samtools view BS.sort.bam | grep -F -f zones.ids > zones.PEs.sam # sorted one maybe more useful.
 290 ```