生物信息學/使用fastp進行數據質量控制
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fastp的特性
編輯- 對數據自動進行全方位質控，生成人性化的報告
- 過濾功能（低質量，太短，太多N……）;
- 對每一個序列的頭部或尾部，計算滑動窗內的質量均值，並將均值較低的子序列進行切除（類似Trimmomatic的做法，但是快非常多）;
- 全局剪裁 （在頭/尾部，不影響去重），對於Illumina下機數據往往最後一到兩個cycle需要這樣處理;
- 去除接頭污染。厲害的是，你不用輸入接頭序列，因為算法會自動識別接頭序列並進行剪裁;
- 對於雙端測序（PE）的數據，軟件會自動查找每一對read的重疊區域，並對該重疊區域中不匹配的鹼基對進行校正;
- 去除尾部的polyG。對於Illumina NextSeq/NovaSeq的測序數據，因為是兩色法發光，polyG是常有的事，所以該特性對該兩類測序平台默認打開;
- 對於PE數據中的overlap區間中不一致的鹼基對，依據質量值進行校正;
- 可以對帶分子標籤（UMI）的數據進行預處理，不管UMI在插入片段還是在index上，都可以輕鬆處理; -可以將輸出進行分拆，而且支持兩種模式，分別是指定分拆的個數，或者分拆後每個文件的行數;
fastp完美支持gzip的輸入和輸出，同時支持SE和PE數據，而且不但支持像Illumina平台的short read數據，也在一定程度上支持了PacBio/Nanopore的long reads數據。
fastp軟件會生成HTML格式的報告，而且該報告中沒有任何一張靜態圖片，所有的圖表都是使用JavaScript動態繪製，非常具有交互性。想要看一下樣板報告的，可以去以下鏈接：http://opengene.org/fastp/fastp.html
而且軟件的開發者還充分考慮到了各種自動化分析的需求，不但生成了人可讀的HTML報告，還生成了程序可讀性非常強的JSON結果，該JSON報告中的數據包含了HTML報告100%的信息，而且該JSON文件的格式還是特殊定製的，不但程序讀得爽，你用任何一款文本編輯器打開，一眼過去也會看得明明白白。想要看一下JSON結果長什麼樣的，可以去以下鏈接：http://opengene.org/fastp/fastp.json
fastp的安裝
編輯Bioconda源安裝
編輯# 不一定最新
conda install -c bioconda fastp
安裝二進制命令
編輯wget http://opengene.org/fastp/fastp
chmod a+x ./fastp
從源碼安裝（Mac和Linux）
編輯git clone https://github.com/OpenGene/fastp.git
# build
cd fastp
make
#安装
sudo make install
從源碼安裝（Windows）
編輯git clone -b master --depth=1 https://github.com/OpenGene/fastp.git
cd fastp
make
fastp的參數和選項
編輯usage: fastp -i <in1> -o <out1> [-I <in1> -O <out2>] [options...]
options:
# I/O options 即输入输出文件设置
-i, --in1 read1 input file name (string)
-o, --out1 read1 output file name (string [=])
-I, --in2 read2 input file name (string [=])
-O, --out2 read2 output file name (string [=])
-6, --phred64 indicates the input is using phred64 scoring (it'll be converted to phred33, so the output will still be phred33)
-z, --compression compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 2. (int [=2])
--reads_to_process specify how many reads/pairs to be processed. Default 0 means process all reads. (int [=0])
# adapter trimming options 过滤序列接头参数设置
-A, --disable_adapter_trimming adapter trimming is enabled by default. If this option is specified, adapter trimming is disabled
-a, --adapter_sequence the adapter for read1. For SE data, if not specified, the adapter will be auto-detected. For PE data, this is used if R1/R2 are found not overlapped. (string [=auto])
--adapter_sequence_r2 the adapter for read2 (PE data only). This is used if R1/R2 are found not overlapped. If not specified, it will be the same as <adapter_sequence> (string [=])
# global trimming options 剪除序列起始和末端的低质量碱基数量参数
-f, --trim_front1 trimming how many bases in front for read1, default is 0 (int [=0])
-t, --trim_tail1 trimming how many bases in tail for read1, default is 0 (int [=0])
-F, --trim_front2 trimming how many bases in front for read2. If it's not specified, it will follow read1's settings (int [=0])
-T, --trim_tail2 trimming how many bases in tail for read2. If it's not specified, it will follow read1's settings (int [=0])
# polyG tail trimming, useful for NextSeq/NovaSeq data polyG剪裁
-g, --trim_poly_g force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
--poly_g_min_len the minimum length to detect polyG in the read tail. 10 by default. (int [=10])
-G, --disable_trim_poly_g disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
# polyX tail trimming
-x, --trim_poly_x enable polyX trimming in 3' ends.
--poly_x_min_len the minimum length to detect polyX in the read tail. 10 by default. (int [=10])
# per read cutting by quality options 划窗裁剪
-5, --cut_by_quality5 enable per read cutting by quality in front (5'), default is disabled (WARNING: this will interfere deduplication for both PE/SE data)
-3, --cut_by_quality3 enable per read cutting by quality in tail (3'), default is disabled (WARNING: this will interfere deduplication for SE data)
-W, --cut_window_size the size of the sliding window for sliding window trimming, default is 4 (int [=4])
-M, --cut_mean_quality the bases in the sliding window with mean quality below cutting_quality will be cut, default is Q20 (int [=20])
# quality filtering options 根据碱基质量来过滤序列
-Q, --disable_quality_filtering quality filtering is enabled by default. If this option is specified, quality filtering is disabled
-q, --qualified_quality_phred the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
-u, --unqualified_percent_limit how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
-n, --n_base_limit if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
# length filtering options 根据序列长度来过滤序列
-L, --disable_length_filtering length filtering is enabled by default. If this option is specified, length filtering is disabled
-l, --length_required reads shorter than length_required will be discarded, default is 15. (int [=15])
# low complexity filtering
-y, --low_complexity_filter enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]).
-Y, --complexity_threshold the threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required. (int [=30])
# filter reads with unwanted indexes (to remove possible contamination)
--filter_by_index1 specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line (string [=])
--filter_by_index2 specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line (string [=])
--filter_by_index_threshold the allowed difference of index barcode for index filtering, default 0 means completely identical. (int [=0])
# base correction by overlap analysis options 通过overlap来校正碱基
-c, --correction enable base correction in overlapped regions (only for PE data), default is disabled
# UMI processing
-U, --umi enable unique molecular identifer (UMI) preprocessing
--umi_loc specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none (string [=])
--umi_len if the UMI is in read1/read2, its length should be provided (int [=0])
--umi_prefix if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default (string [=])
--umi_skip if the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0 (int [=0])
# overrepresented sequence analysis
-p, --overrepresentation_analysis enable overrepresented sequence analysis.
-P, --overrepresentation_sampling One in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20. (int [=20])
# reporting options
-j, --json the json format report file name (string [=fastp.json])
-h, --html the html format report file name (string [=fastp.html])
-R, --report_title should be quoted with ' or ", default is "fastp report" (string [=fastp report])
# threading options 设置线程数
-w, --thread worker thread number, default is 3 (int [=3])
# output splitting options
-s, --split split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0])
-S, --split_by_lines split output by limiting lines of each file with this option(>=1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (long [=0])
-d, --split_prefix_digits the digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding (int [=4])
# help
-?, --help print this message
雖然參數看起來比較多，但常用的主要包括以下幾個部分：
- 輸入輸出文件設置
- 接頭處理
- 全局裁剪（即直接剪掉起始和末端低質量鹼基）
- 滑窗質量剪裁 （與trimmomatic相似）
- 過濾過短序列
- 校正鹼基（用於雙端測序）
- 質量過濾
1、接頭處理
編輯fastp默認啟用了接頭處理，但是可以使用-A命令來關掉。fastp可以自動化地查找接頭序列並進行剪裁，也就是說你可以不輸入任何的接頭序列，fastp全自動搞定了！對於SE數據，你還是可以-a參數來輸入你的接頭，而對於PE數據則完全沒有必要，fastp基於PE數據的overlap分析可以更準確地查找接頭，去得更乾淨，而且對於一些接頭本身就有鹼基不匹配情況處理得更好。fastp對於接頭去除會有一個匯總的報告。
2、全局裁剪
編輯fastp可以對所有read在頭部和尾部進行統一剪裁，該功能在去除一些測序質量不好的cycle比較有用，比如151*2的PE測序中，最後一個cycle通常質量是非常低的，需要剪裁掉。使用-f和-t分別指定read1的頭部和尾部的剪裁，使用-F和-T分別指定read2的頭部和尾部的剪裁。
3、滑窗質量剪裁
編輯很多時候，一個read的低質量序列都是集中在read的末端，也有少部分是在read的開頭。fastp支持像Trimmomatic那樣對滑動窗口中的鹼基計算平均質量值，然後將不符合的滑窗直接剪裁掉。使用-5參數開啟在5』端，也就是read的開頭的剪裁，使用-3參數開啟在3』端，也就是read的末尾的剪裁。使用-W參數指定滑動窗大小，默認是4，使用-M參數指定要求的平均質量值，默認是20，也就是Q20。
4、過濾過短序列
編輯默認開啟多序列過濾，默認值為15，使用-L（--disable_length_filtering）禁止此默認選項。或使用-l（--length_required）自定義最短序列。
5、校正鹼基（用於雙端測序）
編輯fastp支持對PE數據的每一對read進行分析，查找它們的overlap區間，然後對於overlap區間中不一致的鹼基，如果發現其中一個質量非常高，而另一個非常低，則可以將非常低質量的鹼基改為相應的非常高質量值的鹼基值。此選項默認關閉，可使用-c（--correction）開啟。
6、質量過濾
編輯fastp可以對低質量序列，較多N的序列，該功能默認是啟用的，但可以使用-Q參數關閉。使用-q參數來指定合格的phred質量值，比如-q 15表示質量值大於等於Q15的即為合格，然後使用-u參數來指定最多可以有多少百分比的質量不合格鹼基。比如-q 15 -u 40表示一個read最多只能有40%的鹼基的質量值低於Q15，否則會被扔掉。使用-n可以限定一個read中最多能有多少個N。
fastp的使用示例
編輯#!/bin/bash
for i in 74 75 76 82 83 84 85 86 87 88; do
{
fastp -i ~/RNAseq/cleandata/SRR17343${i}_1.fastq.gz -o SRR17343${i}_1.fastq.gz \
-I ~/RNAseq/cleandata/SRR17343${i}_2.fastq.gz -O SRR17343${i}_2.fastq.gz \
-Q --thread=5 --length_required=50 --n_base_limit=6 --compression=6
}&
done
wait