2015-09-08Xiong Xu

fastq文件格式处理工具系列学习

(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






  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 'Output' below
 -v C            Verifies that the 2 files probe id's match up to char C
           use '/' 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 'un1, un2, or join' is appended to the file, or they replace a %-character if present.
   If a 'mate' input file is present (barcode read), then the files'un3' and 'join2' 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