Debian上手動安裝seqtk-1.2-r94

在Debian 8.8上面用apt安裝的seqtk的版本是1.0-r31，要裝比較新版本1.2的步驟如下

STEP 1：到Seqtk的GitHub上面去下載1.2

wget https://github.com/lh3/seqtk/archive/refs/tags/v1.2.tar.gz
md5sum v1.2.tar.gz

計算出來的checksum是 255ffe05bf2f073dc57abcff97f11a37

STEP 2：編譯seqtk-1.2-r94

tar zxf v1.2.tar.gz 
mv seqtk-1.2 /opt/seqtk/1.2 && cd /opt/seqtk/1.2
make seqtk
file seqtk && ldd seqtk

Seqtk編譯後只會出現一個執行檔，不需要做make install，所以把source code也放到 /opt/seqtk/1.2/下面去

seqtk: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, for GNU/Linux 2.6.32, BuildID[sha1]=345fc18b4bb55f9f66efd4cceeb68a178b150a8b, not stripped
    linux-vdso.so.1 (0x00007ffe8174b000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f7779bb9000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f77798b8000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f777950c000)
    /lib64/ld-linux-x86-64.so.2 (0x00005637f683b000)

STEP 3：使用seqtk-1.2-r94

/opt/seqtk/1.2/seqtk

Usage:   seqtk <command> <arguments>
Version: 1.2-r94

Command: seq       common transformation of FASTA/Q
         comp      get the nucleotide composition of FASTA/Q
         sample    subsample sequences
         subseq    extract subsequences from FASTA/Q
         fqchk     fastq QC (base/quality summary)
         mergepe   interleave two PE FASTA/Q files
         trimfq    trim FASTQ using the Phred algorithm

         hety      regional heterozygosity
         gc        identify high- or low-GC regions
         mutfa     point mutate FASTA at specified positions
         mergefa   merge two FASTA/Q files
         famask    apply a X-coded FASTA to a source FASTA
         dropse    drop unpaired from interleaved PE FASTA/Q
         rename    rename sequence names
         randbase  choose a random base from hets
         cutN      cut sequence at long N
         listhet   extract the position of each het

相關資料

• FASTA/Q sequence processing toolkit -- seqtk：演示了下面三項功能
• FASTQ → FASTA
• Reverse complement
• Quality check, 並解釋avgQ, errQ是怎樣計算
• BioLib上面對seqtk的使用說明

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