BBMap can do that!

　　今天碰到一款神器，即BBMap suit. JAVA编写的一套生物信息学工具，可以适用于各种平台。主要是用来进行短序列比对的，但是不仅仅是短序列比对，还有其他很多吊炸天的功能。不仅能够快速比对短序列，还能比对PacBio，454的序列。除了做序列比对和mapping，还有一些非常实用的功能。BBNorm, Dedupe,Reformat,BBduk等工具，下面分别来介绍。
　　首先，说下为啥叫BB呢，因为作者名字首字母缩写就是BB，作者是Brian Bushnell，就是吊，想不到好名字，干脆用自己的名字，这哥们真有勇气，或者自恋？关键关于这个软件，作者迄今还没有发表文章。

BBDuk

　　我们首先来看看BBDuk，他可以用来过滤一些载体序列，污染序列，根据长度，序列质量筛选序列等，具体的见英文（”Duk” stands for Decontamination Using Kmers. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation, subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass. Specifically, any combination of operations is possible in a single pass, with the exception of kmer-based operations (kmer trimming, kmer masking, or kmer filtering); at most 1 kmer-based operation can be done in a single pass. BBDuk2 allows multiple kmer-based operations in a single pass, and is otherwise equivalent to BBDuk.）详细的参数请见命令帮助。