SeqPrep：合并与质控Illumina测序读数-优快云博客

SeqPrep是一款用于合并成对末端Illumina测序读数的工具，尤其适用于有重叠的读数。它还具备适配器修剪功能。在没有适配器序列的情况下，用户可以自定义参数以谨慎合并读数。默认参数适合于预期重叠读数较少的库。程序需要指定的输入和输出fastq文件名。

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一、描述

SeqPrep is a program to merge paired end Illumina reads that areoverlapping into a single longer read. It may also just be used forits adapter trimming feature without doing any paired end overlap.When an adapter sequence is present, that means that the two readsmust overlap (in most cases) so they are forcefully merged. Whenreads do not have adapter sequence they must be treated with carewhen doing the merging, so several user defined parameters for readmerging must be met. The default parameters were chosen withspecificity in mind, so that they could be ran on libraries wherevery few reads are expected to overlap. It is always safest thoughto save the overlapping procedure for libraries where you have someprior knowledge that a significant portion of the reads will havesome overlap. (Description from SeqPrep README file)

SeqPrep是一个程序，用于合并重叠成单个较长读数的成对末端Illumina读数。它也可以仅用于其适配器修剪功能，而不进行任何配对的末端重叠。当存在适配器序列时，这意味着两个读取必须重叠（在大多数情况下），因此强制合并它们。当读取没有适配器序列时，在进行合并时必须小心处理它们，因此必须满足几个用户定义的读取合并参数。选择默认参数时要特别注意，以便它们可以在库中运行，其中很少有读取可能会重叠。尽管保存库的重叠过程总是最安全的，其中您已经知道大部分读取将有一些重叠。（来自SeqPrep README文件的描述）

二、参数

SeqPrep [Required Args][Options]
NOTE 1: The output is always gziped compressed. #输出以gz文件压缩
NOTE 2: If the quality strings in the output contain charactersless than ascii 33 on an ascii table (they look like lines from abinary file), try running again with or without the -6option.
Required Arguments:
Required Arguments:
       -f  first read input fastqfilename         #正链输入文件
       -r second read input fastq filename    #反链输入文件
       -1 first read output fastq filename      #正链输出文件
       -2 second read output fastq filename #反链输出文件