BatVI

简介

检测病毒整合的软件包

安装

通过conda安装

module load miniconda3
conda create -n mypy #创建环境
source activate mypy #进入环境
conda install -c bioconda batvi #安装BatVI

通过链接下载

https://www.comp.nus.edu.sg/~bioinfo/batvi/batvi1.03.tar.gz

#解压
tar -zxvf batvi1.00.tar.gz
cd batvi1.00
./build.sh

使用与范例

CONFIGURATION FILE

在BatVI目录下，创建名为 batviconfig.txt 的文件，文件中的内容如下:

INDEX=< path_to_pathogen_batmis_index >
PATHOGEN_BLAST_DB=< path_to_pathogen_blast_index >
HG_BLAST_DB=< path_to_human_blast_index >
HG_GENOME=< compressed_human_genome >
HG_BWA=< path_to_human_BWA_index >
PATHOGEN_BWA=< path_to_pathogen_BWA_index >
BLAST_PATH=< path_to_blast_binary >
BWA_PATH=< path_to_BWA_binary >
PICARD_PATH=< path_to_picard_jarfiles >
SAMTOOLS_PATH=< path_to_samtools_binary >
BEDTOOLS_PATH=< path_to_bedtools_binary >

batviconfig.txt内容详解如下（可以通过gen_path.sh尝试自动获取路径）:

INDEX is the batmis index of the virus database.
HG_BLAST_DB is the blast index of the virus database.
PATHOGEN_BLAST_DB is the blast index of the human genome.
HG_GENOME contains a compressed version of the human genome.
HG_BWA is the BWA index of human.
PATHOGEN_BWA is the BWA index of the virus database.
BLAST_PATH is the path to the blast binary
BWA_PATH is the path to the BWA binary
PICARD_PATH is the path to the picard jarfiles
SAMTOOLS_PATH is the path to the samtools binary
BEDTOOLS_PATH is the path to the bedtools binary

Example of batviconfig.txt

#This is an example batviconfig.txt file.
#Comments can be written preceded by a hash..
INDEX=/mnt/projects/HBVall/batmis/HBVall.fa
PATHOGEN_BLAST_DB=/mnt/projects/blast/HBVall/HBVall.fa
HG_BLAST_DB=/mnt/projects/blast/hg19/hg19.fa
HG_GENOME=/mnt/projects/hg19/hg19.fa
HG_BWA=/mnt/projects/bwa/hg19/hg19.fa
PATHOGEN_BWA=/mnt/projects/bwa/HBVall/HBVall.fa
BLAST_PATH=/usr/bin
BWA_PATH=/usr/bin
PICARD_PATH=/usr/bin/picard/
SAMTOOLS_PATH=/usr/bin
BEDTOOLS_PATH=/usr/bin

RUNNING THE PROGRAM

准备输入文件

  1. pair-ended fastq files

    A_1.fq
A_2.fq
B_1.fq
B_2.fq

  2. filelist.txt

    A_1.fq;A_2.fq;800
B_1.fq;B_2.fq;800

病毒整合脚本

call_integratons.sh <processing_directory> [ options ]

#processing_directory必须包含filelist.txt，可以包含batviconfig.txt
#options选项
#-l|--log  - Name of the log files to write processing information to
#-t|--threads  - Number of threads to use
#-f|--filterdup - Filter out duplicate reads

OUTPUT FILES AND FORMAT

final_hits.txt

查看输出文件 final_hits.txt 以确认最佳选择，文件内容详解如下:

LIB : Library name
Chr : Chromosome of the human integration
Human Pos : Location of the human integration
Sign : Orientation of the human integration
Viral Sign : Orientation of the viral integration
Viral Pos : Location of the viral integration
Read Count : Number of reads used in the prediction of integration. If the entry is marked MSA, the integration has been found using assembly.
Split Reads : Number of split reads involved in the predicion of the integration. A higher number indicreases the confidence of a prediction.
Uniquely Mapped Reads : Number of unique mappings to the human genome involved in the prediction. A higher number increases the confidence of a prediction.
Multiply Mapped Reads : Number of multiple mappings used in predicting the integration.
Rank1 Hits : Number of reads which have the tophit near the prediction. A higher number increases the confidence of a prediction. The last two columns of this file are to be ignored for this version of BatVI.

predictions.opt.subopt.txt

在文件 predictions.opt.subopt.txt 中查看所有候选位点，predictions.opt.subopt.txt详解如下:

Sign : Orientation of the human integration
Chr : Chromosome of the human integration
Human St : Location of the human integration
Human Ed : Location of the end of the human integration found by reads
Viral Sign : Orientation of the viral integration
Viral St : Location of the viral integration
Viral Ed : Location of the end of the viral integration found by reads
Median_Rank : Median rank of the prediction
Read Count : Number of reads used in the prediction of integration.
Split Reads : Number of split reads involved in the predicion of the integration.
Uniquely Mapped Reads : Number of unique mappings to the human genome involved in the prediction.
Multiply Mapped Reads : Number of multiple mappings used in predicting the integration.
Rank1 Hits : Number of reads which have the tophit near the prediction. The other columns of this file are to be ignored for this version of BatVI.

XXX.predictionsx.msa.txt

在 tmp.batvi/XXX.predictionsx.msa.txt 中查看（XXX即fastq文件所在目录的名称），文件详解如下:

Chr : Chromosome of the human integration
Human Pos : Location of the human integration
Sign : Orientation of the human integration
Viral Pos : Location of the viral integration
Viral Sign : Orientation of the viral integration
Integration type : If the entry is marked TOPHIT, the assembly maps to this location as the best hit. If the entry is marked REPEAT, the assembly can map to at least one other location with similar confidence, and is therefore ambiguous.

范例下载

Example数据下载可使用网址: biogpu.ddns.comp.nus.edu.sg/~ksung/batvi/test

There is a set of test fastq files in the test directory (biogpu.ddns.comp.nus.edu.sg/~ksung/batvi/test). The filelist.txt file is already present. To run a test, a HBV database fasta file is given in HBVall.fa. You can download the hg19 fasta file from UCSC genome browser. After you run the program on this data set, the expected output is given in expected.txt.

注意事项

  • Please ensure that the white spaces in the fasta files and genome names are removed or replaces with a character like an underscore.

  • The index builder bwtformatdb might crash with a message like "Building cached SA index... xxxx/build_index: 47 line: 168087 Segmentation fault (core dump) ....". This is OK as the required indexes would have already been built at this stage.

  • The installation can be cleaned using the command 'build.sh clean '.

  • A directory can be prepared for a fresh run of BatVI with the command 'clean_run.sh '.

参考

最后更新: 2024 年 11 月 22 日