【6.1.2.4】sambamba

官网: https://github.com/biod/sambamba

更多使用案例,参见: https://blog.sciencenet.cn/home.php?mod=space&uid=1094241&do=blog&id=1041577

一、安装

1.1 方法1

下载地址: https://github.com/biod/sambamba/releases

cd /data/software
gunzip sambamba-0.8.2-linux-amd64-static.gz

mkdir bin
mv sambamba-0.8.2-linux-amd64-static sambamba
chmod a+x sambamba

sudo vi /etc/profile
export PATH=/data/software/bin:$PATH

1.2 方法2 (未成功)

先提前安装LDC

需要提前安装LDC (The LDC compiler’s github repository provides binary images. The current preferred release for sambamba is LDC - the LLVM D compiler (>= 1.6.1))

最新版本: https://github.com/ldc-developers/ldc/releases/

cd /data/software
wget -c https://github.com/ldc-developers/ldc/releases/download/v1.29.0/ldc2-1.29.0-linux-x86_64.tar.xz

tar xvJf ldc2-1.29.0-linux-x86_64.tar.xz

export PATH=/data/software/ldc2-1.29.0-linux-x86_64/bin:$PATH
export LIBRARY_PATH=/data/software/ldc2-1.29.0-linux-x86_64/lib:$LIBRARY_PATH

另一个版本:

wget -c https://github.com/ldc-developers/ldc/releases/download/v1.7.0/ldc2-1.7.0-linux-x86_64.tar.xz

tar xvJf ldc2-1.7.0-linux-x86_64.tar.xz

export PATH=/data/software/ldc2-1.7.0-linux-x86_64/bin:$PATH
export LIBRARY_PATH=/data/software/ldc2-1.7.0-linux-x86_64/lib:$LIBRARY_PATH

第三个版本

wget -c https://github.com/ldc-developers/ldc/releases/download/v1.15.0/ldc2-1.15.0-linux-x86_64.tar.xz

tar xvJf ldc2-1.15.0-linux-x86_64.tar.xz

export PATH=/data/software/ldc2-1.15.0-linux-x86_64/bin:$PATH
export LIBRARY_PATH=/data/software/ldc2-1.15.0-linux-x86_64/lib:$LIBRARY_PATH

三个版本始终报错报错:

ldc2: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by ldc2)
ldc2: /lib64/libc.so.6: version `GLIBC_2.18' not found (required by ldc2)

需要安装新版的glibc, https://ftp.gnu.org/gnu/glibc/ 。 但没有成功

再安装sambamba

git clone --recursive https://github.com/biod/sambamba.git
cd /data/software/sambamba-master
cd sambamba
make

二、用法

(base) [sam@c01 1.no_trim]$ sambamba --help

sambamba 0.8.2
 by Artem Tarasov and Pjotr Prins (C) 2012-2021
    LDC 1.27.1 / DMD v2.097.2 / LLVM11.0.0 / bootstrap LDC - the LLVM D compiler (1.27.1)


Usage: sambamba [command] [args...]

  Available commands:

    view        view contents and convert from one format
                to another (SAM/BAM/JSON/UNPACK)
    index       build index (BAI)
    merge       merge files (BAM)
    sort        sort file (BAM)
    slice       slice file (BAM using BED)
    markdup     mark or remove duplicates (BAM)
    subsample   subsample (BAM)
    flagstat    output statistics (BAM)
    depth       output statistics (BAM)
    validate    simple validator (BAM)

  No longer recommended:

    mpileup     parallel execution of samtools (BAM)

To get help on a particular command, call it without args.

Global options

    -q          quiet mode (do not show banner)

For bug reports and feature requests see

       https://github.com/biod/

三、我的案例

sam转bam

sambamba view -S -t 100 -f=bam  198p.sam -o 198pr.bam

排序bam

sambamba sort 198pr.bam -o 198pr.sorted.bam -t 150

bam建Index

sambamba index 198pr.sorted.bam -t 150
个人公众号,比较懒,很少更新,可以在上面提问题,如果回复不及时,可发邮件给我: tiehan@sina.cn