去除reads中的pcr 重复，fastquniq

改编：

python ~/tools2assemble/run_fastuniq.py SHT-3K-1_1.fq.gz SHT-3K-1_2.fq.gz

好像不支持gz文件，要先解压

http://sourceforge.net/projects/fastuniq/

下载：

http://sourceforge.net/projects/fastuniq/files/FastUniq-1.1.tar.gz/download

如果下载下来文件名是download 改一下名字 这是个tar.gz文件。

cd FastUniq/

cd source/

make

这个文件夹下的fastuniq就可以用了

FastUniq Program parameters:
==========================================================================

-i : The input file list of paired FSATQ sequence files [FILE IN]
Maximum 1000 pairs

This parameter is used to specify a list of paired sequence files in
FASTQ format as input, in which two adjacent files with reads in the
same order belong to a pair.

-t : Output sequence format [q/f/p]
q : FASTQ format into TWO output files
f : FASTA format into TWO output files
p : FASTA format into ONE output file
default = q

This parameter is used to specify sequence format in output file(s).
FastUniq could output read pairs into two files in either FASTQ [q]
or FASTA [f] format, in which reads in the same order belonging to a
pair. FastUniq could also output read pairs into a single file in
FASTA format [p], in which adjacent reads belonging to a pair.

-o : The first output file [FILE OUT]

-p : The second output file [FILE OUT]
Optional. ONLY required when output sequence format(-t) is specify as
[q] or [f].

-c : Types of sequence descriptions for output [0/1]
0 : The raw descriptions
1 : New serial numbers assigned by FastUniq
default = 0

举例：

~/FastUniq/source/fastuniq -i fq_list.txt -o out1 -p out2

改编：

python ~/tools2assemble/run_fastuniq.py SHT-3K-1_1.fq.gz SHT-3K-1_2.fq.gz

freemao

FAFU