fastq文件格式处理工具系列学习

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

fastq文件格式说明（wiki）

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

fastq 文件质量控制

fastqc

CommandLine Demo：./FastQC/fastqc -o ./ –extract -f fastq -t 4 -q file.fq.gz
solexaQA
Dependency：R, gcc, perl
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。
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
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
```

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

seqtk
Dependency: gcc
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.
SeqPrep
homerTools
http://homer.salk.edu/homer/ngs/homerTools.html
http://homer.salk.edu/homer/basicTutorial/fastqFiles.html

fastq压缩

BEETL-fastq
http://arxiv.org/pdf/1406.4376v1.pdf
fastqz
scalce
DSRC

模拟生成fastq格式文件

wgsim

Program: wgsim (short read simulator)Version: 0.3.0Contact: 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

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

Pair End read 连接

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 versionOutput:  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.

COPE
http://bioinformatics.oxfordjournals.org/content/early/2012/10/08/bioinformatics.bts563.full.pdf
PEAR
FLASH
http://ccb.jhu.edu/software/FLASH/FLASH-reprint.pdf
fastq文件数据纠错（基于K-mer）
reptile
Dependency：make, g++, perl
https://code.google.com/p/ngopt/wiki/ReptileErrorCorrection
quake
LSC for PacBio long read error correction