HTSlib + Samtools + BCFtools

  1. # PWD=/home/chenshulin/workspace/bin
  3. # htslib
  4. git clone https://github.com/samtools/htslib.git
  5. cd htslib/
  6. autoheader
  7. autoconf
  8. ./configure --prefix=/home/chenshulin/workspace/bin/htslib/
  9. make 
  10. make install
  11. cd ..
  13. # samtools
  14. git clone https://github.com/samtools/samtools.git
  15. cd samtools/
  16. autoheader
  17. ./configure --prefix=/home/chenshulin/workspace/bin/samtools/
  18. make
  19. make install
  20. cd ..
  22. # bcftools
  23. git clone https://github.com/samtools/bcftools.git
  24. cd bcftools/
  25. autoheader
  26. autoconf
  27. ./configure --prefix=/home/chenshulin/workspace/bin/samtools/ --enable-libgsl --enable-perl-filters
  28. make 
  29. make install
  30. cd ..

PICARD

  1. wget https://github.com/broadinstitute/picard/releases/download/2.22.4/picard.jar
  3. # 测试
  4. java -jar picard.jar

BWA

  1. git clone https://github.com/lh3/bwa.git
  2. cd bwa
  3. make

GATK

  1. wget https://github.com/broadinstitute/gatk/releases/download/4.1.7.0/gatk-4.1.7.0.zip
  2. unzip gatk-4.1.7.0.zip
  3. cd gatk-4.1.7.0/
  4. ./gatk --list

VEP

Varscan

  1. git clone https://github.com/dkoboldt/varscan.git
  2. cd varscan/
  3. java -jar Varscan.v2.4.4.jar

BEDtools

  1. wget -c https://github.com/arq5x/bedtools2/releases/download/v2.29.2/bedtools.static.binary
  2. mv bedtools.static.binary bedtools
  3. chmod +x bedtools
  4. ./bedtools

Strelka

  1. # download strelka binary
  2. wget https://github.com/Illumina/strelka/releases/download/v2.9.2/strelka-2.9.2.centos6_x86_64.tar.bz2
  3. # decompress
  4. tar xvjf strelka-2.9.2.centos6_x86_64.tar.bz2
  5. # run demo to check successful installation
  6. bash strelka-2.9.2.centos6_x86_64/bin/runStrelkaSomaticWorkflowDemo.bash
  7. bash strelka-2.9.2.centos6_x86_64/bin/runStrelkaGermlineWorkflowDemo.bash

Sambamba

  1. git clone https://github.com/genome/bam-readcount.git
  2. cd bam-readcount/
  3. cmake .
  4. make
  5. ./bin/bam-readcount

HISAT2

  1. wget -O hisat2-2.2.0-Linux_x86_64.zip https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-Linux_x86_64/download
  2. unzip hisat2-2.2.0-Linux_x86_64.zip
  3. cd hisat2-2.2.0/
  4. ./hisat2

StringTie

Gffcompare

CNVnator

CNVkit

Kallisto

Pizzly

Manta

mosdepth

bam-readcount

vt

seqtk

seqkit

fastqc

multiQC

vcf-annotation-tools