Bioinformatics Armory第16题：Base Filtration by Quality

Problem

Bad quality bases can be easily trimmed out using certain threshold (defined by quality plot similar to what we did in “Base Quality Distribution”) There is a lot of trimming tools, you can try one of following:

• FASTQ Quality Trimmer tool on the Galaxy. It uses a "sliding window" approach so for a simple trimming of the ends you should set window size 1.

• Trimmomatic. It is a command-line java-based tool, detail description and download link can be found here. For a simple trimming from both ends you should specify parameters LEADING and TRAILING.

Given: FASTQ file, quality cut-off value , Phred33 quality score assumed.

Return: FASTQ file trimmed from the both ends (removed leading and trailing bases with quality lower than )

可以使用特定阈值轻松修剪掉质量差的基准（由质量图定义，类似于我们在“基本质量分布”中所做的定义）修剪工具很多，您可以尝试以下方法之一：

• Galaxy上的FASTQ Quality Trimmer工具。它使用“滑动窗口”方法，因此，为简单修整两端，应将窗口大小设置为1。

• Trimmomatic。这是一个基于Java的命令行工具，详细说明和下载链接可以在此处找到。为了从两端进行简单修整，应指定参数LEADING和TRAILING。

给出： FASTQ文件，质量截止值，假定为Phred33质量得分。

返回值：从两端修剪的FASTQ文件（删除质量低于）

Sample Dataset

20
@Rosalind_0049
GCAGAGACCAGTAGATGTGTTTGCGGACGGTCGGGCTCCATGTGACACAG
+
FD@@;C<AI?4BA:=>C<G=:AE=><A??>764A8B797@A:58:527+,
@Rosalind_0049
AATGGGGGGGGGAGACAAAATACGGCTAAGGCAGGGGTCCTTGATGTCAT
+
1<<65:793967<4:92568-34:.>1;2752)24')*15;1,.3*3+*!
@Rosalind_0049
ACCCCATACGGCGAGCGTCAGCATCTGATATCCTCTTTCAATCCTAGCTA
+
B:EI>JDB5=>DA?E6B@@CA?C;=;@@C:6D:3=@49;@87;::;;?8+

Sample Output

@Rosalind_0049
GCAGAGACCAGTAGATGTGTTTGCGGACGGTCGGGCTCCATGTGACAC
+
FD@@;C<AI?4BA:=>C<G=:AE=><A??>764A8B797@A:58:527
@Rosalind_0049
ATGGGGGGGGGAGACAAAATACGGCTAAGGCAGGGGTCCT
+
<<65:793967<4:92568-34:.>1;2752)24')*15;
@Rosalind_0049
ACCCCATACGGCGAGCGTCAGCATCTGATATCCTCTTTCAATCCTAGCT
+
B:EI>JDB5=>DA?E6B@@CA?C;=;@@C:6D:3=@49;@87;::;;?8