bioinformatics tools installation (2023 최신버전)

BI 분석에서 대표적으로 사용되는 툴들의
설치 방법에 대해 알아보겠습니다.
설치 대상은 아래와 같습니다.

- bedtools2
- samtools-1.16.1
- bcftools-1.16
-HTSlib-1.16
- sickle-1.33
- bwa-mem2
- gatk-4.3.0.0

git clone, wget 명령어를 통해서 파일을 다운받아서 설치 하겠습니다.
( centos 운영체제를 사용하고 있습니다. )

다운 받고자하는 디렉토리로 이동하시고 아래 cmd 를 입력하시면 됩니다.

 [skkwon1048@server Tools]$ pwd
/data/Tools

 

1. BEDTOOLS

$ wget https://github.com/arq5x/bedtools2/releases/download/v2.29.1/bedtools-2.29.1.tar.gz
$ tar -zxvf bedtools-2.29.1.tar.gz
$ cd bedtools2
$ make

$ cd bedtools2/bin
$ ./bedtools
#작동 확인

bedtools is a powerful toolset for genome arithmetic.

Version:   v2.30.0
About:     developed in the quinlanlab.org and by many contributors worldwide.
Docs:      http://bedtools.readthedocs.io/
Code:      https://github.com/arq5x/bedtools2
Mail:      https://groups.google.com/forum/#!forum/bedtools-discuss

Usage:     bedtools <subcommand> [options]

The bedtools sub-commands include:

 

https://bedtools.readthedocs.io/en/latest/content/installation.html

Installation — bedtools 2.30.0 documentation

 

2. SAMTOOLS

$ wget https://github.com/samtools/samtools/releases/download/1.16.1/samtools-1.16.1.tar.bz2
$ tar -vxjf samtools-1.16.1.tar.bz2
$ cd samtools-1.16.1
$ make

$ cd samtools-1.16.1
$ ./samtools
#작동확인

Program: samtools (Tools for alignments in the SAM format)
Version: 1.16.1 (using htslib 1.16)

Usage:   samtools <command> [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     fqidx          index/extract FASTQ
     index          index alignment

http://www.htslib.org/download/

SAMtools/BCFtools/HTSlib - Downloads

 

3. BCFTOOLS

$ wget https://github.com/samtools/bcftools/releases/download/1.16/bcftools-1.16.tar.bz2
$ tar -vxjf bcftools-1.9.tar.bz2
$ cd bcftools-1.9
$ make

$ cd bcftools-1.16
$ ./bcftools
#작동확인

Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Version: 1.16 (using htslib 1.16)

Usage:   bcftools [--version|--version-only] [--help] <command> <argument>

Commands:

 -- Indexing
    index        index VCF/BCF files

 -- VCF/BCF manipulation
    annotate     annotate and edit VCF/BCF files
    concat       concatenate VCF/BCF files from the same set of samples
    convert      convert VCF/BCF files to different formats and back
    head         view VCF/BCF file headers

http://www.htslib.org/download/

SAMtools/BCFtools/HTSlib - Downloads

 

4. HTSlib

$ wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 -O htslib.tar.bz2
$ tar -xjvf htslib.tar.bz2
$ cd htslib-1.16
$ make

$ cd htslib-1.16
$ ./htslib
#작동확인

http://www.htslib.org/download/

SAMtools/BCFtools/HTSlib - Downloads

 

Export To Path And Refresh

시스템변수를 지정하면, 툴실행할때

절대경로를 이용하거나 working directory 에 가서 실행해야하는

번거로움을 해결 할 수 있습니다.

export PATH="$PATH:/usr/bin/bcftools-1.16"
export PATH="$PATH:/usr/bin/samtools-1.16.1"
export PATH="$PATH:/usr/bin/htslib-1.16"
source ~/.profile

 

5. SICKLE

$ https://github.com/najoshi/sickle/archive/refs/tags/v1.33.tar.gz
$ tar -zxvf sickle-1.33.tar.gz
$ cd
$ make

$ cd sickle-1.33
$ ./sickle
#작동확인

Usage: sickle <command> [options]

Command:
pe      paired-end sequence trimming
se      single-end sequence trimming

https://github.com/najoshi/sickle/releases

Releases · najoshi/sickle

 

6. BWA MEM2

$ git clone https://github.com/bwa-mem2/bwa-mem2
$ cd bwa-mem2
$ git submodule init
$ git submodule update
# Compile and run
$ make
$ ./bwa-mem2

cd bwa-mem2
./bwa-mem2
#작동확인

Looking to launch executable "/data/Tools/align/bwa-mem2/./bwa-mem2.avx2", simd = .avx2
Launching executable "/data/Tools/align/bwa-mem2/./bwa-mem2.avx2"
Usage: bwa-mem2 <command> <arguments>
Commands:
  index         create index
  mem           alignment
  version       print version number

https://github.com/bwa-mem2/bwa-mem2

GitHub - bwa-mem2/bwa-mem2: The next version of bwa-mem

Difference between mem and mem2
mem 과 mem2 성능 비교한 포스팅이 있어서 참고하시면 유용한 정보가 될듯합니다.
https://oyat.nl/bwa2/

Running bwa vs bwa-mem2 – Oyat consulting

 

7. GATK4

$ wget https://github.com/broadinstitute/gatk/releases/download/4.3.0.0/gatk-4.3.0.0.zip
$ unzip gatk-4.3.0.0.zip 
$ cd gatk-4.3.0.0
$ ./gatk
#작동확인

 Usage template for all tools (uses --spark-runner LOCAL when used with a Spark tool)
    gatk AnyTool toolArgs

 Usage template for Spark tools (will NOT work on non-Spark tools)
    gatk SparkTool toolArgs  [ -- --spark-runner <LOCAL | SPARK | GCS> sparkArgs ]

 Getting help
    gatk --list       Print the list of available tools

    gatk Tool --help  Print help on a particular tool

 Configuration File Specification
     --gatk-config-file                PATH/TO/GATK/PROPERTIES/FILE

 gatk forwards commands to GATK and adds some sugar for submitting spark jobs

   --spark-runner <target>    controls how spark tools are run
     valid targets are:
     LOCAL:      run using the in-memory spark runner
     SPARK:      run using spark-submit on an existing cluster
                 --spark-master must be specified
                 --spark-submit-command may be specified to control the Spark submit command
                 arguments to spark-submit may optionally be specified after --
     GCS:        run using Google cloud dataproc
                 commands after the -- will be passed to dataproc
                 --cluster <your-cluster> must be specified after the --
                 spark properties and some common spark-submit parameters will be translated
                 to dataproc equivalents

   --dry-run      may be specified to output the generated command line without running it
   --java-options 'OPTION1[ OPTION2=Y ... ]'   optional - pass the given string of options to the
                 java JVM at runtime.
                 Java options MUST be passed inside a single string with space-separated values.

   --debug-port <number> sets up a Java VM debug agent to listen to debugger connections on a
                         particular port number. This in turn will add the necessary java VM arguments
                         so that you don't need to explicitly indicate these using --java-options.
   --debug-suspend       sets the Java VM debug agent up so that the run get immediatelly suspended
                         waiting for a debugger to connect. By default the port number is 5005 but
                         can be customized using --debug-port

https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4


Bioinformatics 분석에 대표적으로 사용되는 툴 설치 방법에 대해 알아보았습니다.
각 툴들에서 다양한 옵션들과 기능들을 파악해보면 좋을듯 합니다.
다음에 또 찾아뵙겠습니다 :)