skewer过滤软件的安装及使用

skewer 是一个能快速且准确地处理NGS双端reads的接头去除软件。

一、安装软件

conda install -c bioconda skewer=v0.2.2

二、skewer命令参数详解

USAGE: skewer [options]  [paired-reads.fastq]
    or skewer [options] - (for input from STDIN)

OPTIONS (ranges in brackets, defaults in parentheses):
 Adapter:
          -x  Adapter sequence/file (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)  ##接头序列文件
          -y  Adapter sequence/file for pair-end reads (AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA),  ##双端序列的接头序列文件
                   implied by -x if -x is the only one specified explicitly.
          -M, --matrix  File indicates valid adapter pairing (all-ones matrix).
          -j  Junction adapter sequence/file for Nextera Mate Pair reads (CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG)
          -m, --mode  trimming mode; 1) single-end -- head: 5' end; tail: 3' end; any: anywhere (tail)
                           2) paired-end -- pe: paired-end; mp: mate-pair; ap: amplicon (pe)
          -b, --barcode    Demultiplex reads according to adapters/primers (no)
 Tolerance:
          -r  Maximum allowed error rate (normalized #errors / length of aligned region) [0, 0.5], (0.1)   ##允许的最大错误率
          -d  Maximum allowed indel error rate [0, r], (0.03)   ##允许的最大插入或缺失错误率
                   reciprocal is used for -r, -e and -d when num > or = 2
          -k  Minimum overlap length for adapter detection [1, inf);
                   (max(1, int(4-10*r)) for single-end; (/2) for mate-pair)
 Clipping:
          -c, --cut , Hard clip off the 5' leading bases as the barcodes in amplicon mode; (no)
          -e, --cut3            Hard clip off the 3' tailing bases if the read length is greater than
                                the maximum read length specified by -L; (no)
 Filtering:
          -q, --end-quality   Trim 3' end until specified or higher quality reached; (0)   ## 3'端末尾碱基质量
          -Q, --mean-quality  The lowest mean quality value allowed before trimming; (0)  ##最小平均质量值
          -l, --min  The minimum read length allowed after trimming; (18)  ##过滤后最小read长度
          -L, --max  The maximum read length allowed after trimming; (no limit)  ##过滤后最大read长度
          -n  Whether to filter out highly degenerative (many Ns) reads; (no)  ## 是否过滤掉含有许多N的reads
          -u  Whether to filter out undetermined mate-pair reads; (no)  
          -N, --fillNs Whether to replace trimmed bases with Ns (has no effect with 'b' or '-m mp'); (no)
 Input/Output:
          -f, --format    Format of FASTQ quality value: sanger|solexa|auto; (auto)  ##FASTQ质量值的输出格式，默认自动
          -o, --output    Base name of output file; ('.trimmed')  ## 输出文件的前缀名
          -z, --compress       Compress output in GZIP format (no)  ##以压缩格式GZIP输出
          -1, --stdout         Redirect output to STDOUT, suppressing -b, -o, and -z options (no)
          --qiime              Prepare the "barcodes.fastq" and "mapping_file.txt" for processing with QIIME; (default: no)
          --quiet              No progress update (not quiet)
          -A, --masked-output  Write output file(s) for trimmed reads (trimmed bases converted to lower case) (no)
          -X, --excluded-output Write output file(s) for excluded reads (no)
 Miscellaneous:
          -i, --intelligent     For mate-pair mode, whether to redistribute reads based on junction information; (no)
          -t, --threads    Number of concurrent threads [1, 32]; (1)   ##运行线程数

三、示例

EXAMPLES:
          skewer -Q 9 -t 2 -x adapters.fa sample.fastq -o trimmed
          skewer -x AGATCGGAAGAGC -q 3 sample-pair1.fq.gz sample-pair2.fq.gz
          skewer -x TCGTATGCCGTCTTCTGCTTGT -l 16 -L 30 -d 0 srna.fastq
          skewer -m mp -i lmp-pair1.fastq lmp-pair2.fastq
          skewer -m ap --cut 0,6 --qiime -x forward-primers.fa -y reverse-primers.fa mix-pair1.fastq mix-pair2.fastq
          ##双端序列过滤，输出结果如下图所示：
          skewer -m pe -q 3 -l 30 -n -z ./raw_reads/ERR3209755_1.fastq.gz ./raw_reads/ERR3209755_2.fastq.gz -o ./trimmed_reads/ERR3209755

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