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] <reads.fastq> [paired-reads.fastq]
or skewer [options] - (for input from STDIN)
OPTIONS (ranges in brackets, defaults in parentheses):
Adapter:
-x <str> Adapter sequence/file (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) ##接头序列文件
-y <str> 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 <str> File indicates valid adapter pairing (all-ones matrix).
-j <str> Junction adapter sequence/file for Nextera Mate Pair reads (CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG)
-m, --mode <str> 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 <num> Maximum allowed error rate (normalized #errors / length of aligned region) [0, 0.5], (0.1) ##允许的最大错误率
-d <num> 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 <int> Minimum overlap length for adapter detection [1, inf);
(max(1, int(4-10*r)) for single-end; (<junction length>/2) for mate-pair)
Clipping:
-c, --cut <int>,<int> 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 <int> Trim 3' end until specified or higher quality reached; (0) ## 3'端末尾碱基质量
-Q, --mean-quality <int> The lowest mean quality value allowed before trimming; (0) ##最小平均质量值
-l, --min <int> The minimum read length allowed after trimming; (18) ##过滤后最小read长度
-L, --max <int> 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 <str> Format of FASTQ quality value: sanger|solexa|auto; (auto) ##FASTQ质量值的输出格式，默认自动
-o, --output <str> Base name of output file; ('<reads>.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 <int> 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
image.png
