fastq文件格式处理工具系列学习

转自：http://ju.outofmemory.cn/entry/215236

fastq文件格式说明（wiki）

1. FASTQ_format 维基百科
2. NSC_2011_Illumina_fastqAndQC Illumina fastq 格式官方文档

fastq 文件质量控制

1. fastqc 
    
   CommandLine Demo：./FastQC/fastqc -o ./ –extract -f fastq -t 4 -q file.fq.gz

2. solexaQA 
   Dependency：R, gcc, perl

   

   
   
   
   
   
   

3. fastx toolkit 
   Dependency: g++, PerlIO::gzip, GD::Graph::bars, sed, gnuplot

   • fastx_clipper: 
     截3’端 adaptor的程序，仅支持单端测序
   • fastx_trimmer: 
     截取位于start-end区间，或者从末端截掉一定长度的序列，输出fastq格式
   • fastx_quality_stats: 
     输出质量值统计结果，可用fastq_quality_boxplot_graph.sh做质量值boxplot图 
     
   • fastq_to_fasta: 
     将fastq转换成fasta格式
   • fastq_quality_filter: 
     根据质量值筛选过滤，质量值低于cutoff的将被过滤掉
   • fastq_quality_trimmer: 
     根据质量值截取序列，质量值低的3’ end部分将会被截短，如果截取之后剩余长度不足最小长度阈值，则这条read将会被过滤掉
   • fastx_reverse_complement: 
     取反向互补序列
   • fastx_collapser: 
     输出每条序列及其出现的频数（duplication level）
   • fastx_uncollapser: 
     输出文件参数为fastx_collapser的输出文件，将出现多少次的序列输出多少次
   • fasta_formatter: 
     主要要用来控制输出fasta格式文件每行的序列长度
   • fasta_nucleotide_changer: 
     主要用来切换T与U碱基（DNA/RNA）模式
   • fastx_renamer: 
     用read序号数作为read name
   • fastq_masker: 
     将read中低于质量值阈值的碱基 mask成其他字符（’.’ or ‘N’）
   • fastx_nucleotide_distribution_line_graph.sh: 
     输入文件为fastx_quality_stats的输出结果，用于画所有reads在每个cycle的碱基含量分布线形图
   • fastx_nucleotide_distribution_graph.sh： 
     同上，做stacked barplot图 
      
     根据fastq文件的5‘end or 3’end 固定长度的序列种类，来分割子文件，可容mismatch容gap
   • fasta_clipping_histogram.pl: 
     对fastx_clipper, fastx_trimmer, fastq_quality_trimmer处理的结果做统计，画长度分布图。 
     
4. fastq-tools 
   Dependency: gcc，prce
   • fastq-grep: find reads matching a regular-expression
   • fastq-kmers: count k-mer occurances
   • fastq-match: local alignment of a sequence to each read
   • fastq-sample: randomly sample reads with or without replacement
   • fastq-sort: sort fastq files
   • fastq-uniq: filter reads with identical sequences

5. flexbar 
   http://sourceforge.net/p/flexbar/wiki/Manual/

   • Description: 
     flexbar支持多线程 adaptor clipper，支持Pair End,支持 barcode trimmer,支持多种截取模式

   • Dependency:

     • g++
     • tbb 为并行任务 设计的c++模板库
     • seqan 有名的生物数据处理 C++底层库，提供多种文件格式、数据结构和算法支持

   • CommandLine Demo:

     flexbar -n 4 -at 2 -u 1 -m 20 -ao 5 -f i1.8 -a $adaptor --reads $indir/$fastq1 --reads2 $indir/$fastq2 -z GZ -t $outfile_prefix > $outfile_prefix.flexbar.log

6. trimmomatic A flexible read trimming tool for Illumina NGS data 
   Dependency: java

   • Pair End Demo:

     java -jar trimmomatic-0.30.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

   • Single End Demo:

     java -jar trimmomatic-0.30.jar SE -phred33 input.fq.gz output.fq.gz ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

7. seqtk 
   Dependency: gcc
8. Fqutils 
   Dependency: gcc
   • fqu_are_paired 
     Checks if two files are associated pairwise: Does the first record appearing in FASTQ file_1 have the same identifier as the first record in FASTQ file_2? …, etc.
   • fqu_cat 
     Like Unix cat, but for files in FASTQ format. Assuming well-formed input the output is guaranteed to be in lazy-FASTQ records. Especially useful when your own parsers assume this simpler format.
   • fqu_cull 
     Reports a subset of a FASTQ stream, based on a collection of identifiers.
   • fqu_degen 
     Replaces A, C, G, T with degenerate codes. Options include conversion to purines and pyrimidines (A, G -> R and C, T -> Y) and to a GC representation (C, G -> S and A, T -> W).
   • fqu_rselect 
     Randomly select a subset of records from FASTQ input.
   • fqu_splitq 
     Segregate FASTQ input into two output files, based on a collection of identifiers.
   • fqu_summary 
     Generate summary statistics for FASTQ input. These include total record (sequence) count, maximum sequence size, a estimation of the quality offset (33 or 64), basecounts per position, a GC content histogram, and per position quartiles of the qualities.
   • fqu_tidy 
     Write FASTQ output based on FASTQ input. Like fqu_cat, output is guaranteed to be in four line records. Provides a “–squash” option for reducing the size of each record, currently by ignoring the second header, and a “–tab-delimited” option if you happen to want the output stream in a four column format. These single line records can be particularly convenient for internal processing pipelines.
   • fqu_wc 
     Generates word (kmer) counts for FASTQ input.
9. SeqPrep
10. homerTools 
    http://homer.salk.edu/homer/ngs/homerTools.html 
    http://homer.salk.edu/homer/basicTutorial/fastqFiles.html

fastq压缩

1. BEETL-fastq 
   http://arxiv.org/pdf/1406.4376v1.pdf
2. fastqz
3. scalce
4. DSRC

模拟生成fastq格式文件

1. XS

2. wgsim

   Program: wgsim (short read simulator)
   Version: 0.3.0
   Contact: Heng Li <lh3@sanger.ac.uk>
   Usage:   wgsim [options] <in.ref.fa> <out.read1.fq> <out.read2.fq>
   Options: -e FLOAT      base error rate [0.020]
            -d INT        outer distance between the two ends [500]
            -s INT        standard deviation [50]
            -N INT        number of read pairs [1000000]
            -1 INT        length of the first read [70]
            -2 INT        length of the second read [70]
            -r FLOAT      rate of mutations [0.0010]
            -R FLOAT      fraction of indels [0.15]
            -X FLOAT      probability an indel is extended [0.30]
            -S INT        seed for random generator [-1]
            -h            haplotype mode

k-mer计数

1. khmer
2. KMC
3. JELLYFISH 
   genome size estimating based on kmer-counting https://github.com/josephryan/estimate\_genome\_size.pl
4. BF Counter

Pair End read 连接

1. fastq-join

   Usage: fastq-join [options] <read1.fq> <read2.fq> [mate.fq] -o <read.%.fq>
   Joins two paired-end reads on the overlapping ends.
   Options:
   -o FIL          See &apos;Output&apos; below
   -v C            Verifies that the 2 files probe id&apos;s match up to char C
             use &apos;/&apos; for Illumina reads
   -p N            N-percent maximum difference (8)
   -m N            N-minimum overlap (6)
   -r FIL          Verbose stitch length report
   -R              No reverse complement
   -V              Show version
   Output:
     You can supply 3 -o arguments, for un1, un2, join files, or one argument as a file name template.  The suffix &apos;un1, un2, or join&apos; is appended to the file, or they replace a %-character if present.
     If a &apos;mate&apos; input file is present (barcode read), then the files&apos;un3&apos; and &apos;join2&apos; are also created.
     Files named ".gz" are assumed to be compressed, and can be read/written as long as "gzip" is in the path.

2. COPE 
   http://bioinformatics.oxfordjournals.org/content/early/2012/10/08/bioinformatics.bts563.full.pdf
3. PEAR
4. FLASH 
   http://ccb.jhu.edu/software/FLASH/FLASH-reprint.pdf

   fastq文件数据纠错（基于K-mer）

5. reptile 
   Dependency：make, g++, perl 
   https://code.google.com/p/ngopt/wiki/ReptileErrorCorrection
6. quake
7. LSC for PacBio long read error correction

(本文由GeneDock公司 Senior Bioinformatics Engineer 许雄撰写，转载请保留作者信息和原文链接)

fastq文件格式说明（wiki）

1. FASTQ_format 维基百科
2. NSC_2011_Illumina_fastqAndQC Illumina fastq 格式官方文档

fastq 文件质量控制

1. fastqc 
    
   CommandLine Demo：./FastQC/fastqc -o ./ –extract -f fastq -t 4 -q file.fq.gz

2. solexaQA 
   Dependency：R, gcc, perl