fastq文件基本信息统计工具

之前写的一个小工具，写的很简陋，名字取的也很随意就叫skr，哈哈。主要是fq转fa、合并多个染色体的vcf文件等，功能不多（主要是C写起来太操蛋了T_T），通常我也只用来统计fastq文件信息：

这里给出工具地址：https://github.com/sharkLoc/skrTools 

安装：

git clone https://github.com/sharkLoc/skrTools.git
cd skrTools && make 

usage：

Program: skr 

Usage: skr <command> [options]

    fq2fa      translate fastq file to fasta
    fqstat     summary statistics of fastq file
    mergeVcf   merge vcf files from list
    statVcf    summary statistics of vcf file
    makewind   make bed from a list file

 

统计fastq文件信息：

输出read的平均长度，GC含量，总read数量和总的碱基数量，当然还包括ATGC和N碱基的数量和百分比，最后就是Q20和Q30结果。

skr fqstat -i xx1.fq.gz -I xx2.fq.gz

输出文件：

Iterm    reads_1.fq    reads_2.fq
read average length:    150    150
read GC content(%):    48.42    48.48
total read Count:    34946389    34946389
total base Count:    5241958350    5241958350

base A Count:    1352284833(25.80%)    1342903044(25.62%)
base C Count:    1270459966(24.24%)    1246706604(23.78%)
base G Count:    1267522866(24.18%)    1294357728(24.69%)
base T Count:    1351401800(25.78%)    1357986115(25.91%)
base N Count:    288885(0.01%)    4859(0.00%)

Number of base calls with quality value of 20 or higher (Q20+) (%)    5113248711(97.54%)    5092440219(97.15%)
Number of base calls with quality value of 30 or higher (Q30+) (%)    4886887711(93.23%)    4832524601(92.19%)