seqtk

seqtk:lh3/seqtk: Toolkit for processing sequences in FASTA/Q formats (github.com)

seqtk的使用说明 - 简书 (jianshu.com):

$ ${seqtk_dir}/seqtk-1.2/seqtk
==============================================================
Usage:   seqtk <command> <arguments>
Version: 1.2-r94

Command: seq       common transformation of FASTA/Q
         comp      get the nucleotide composition of FASTA/Q
         sample    subsample sequences
         subseq    extract subsequences from FASTA/Q
         fqchk     fastq QC (base/quality summary)
         mergepe   interleave two PE FASTA/Q files
         trimfq    trim FASTQ using the Phred algorithm

         hety      regional heterozygosity
         gc        identify high- or low-GC regions
         mutfa     point mutate FASTA at specified positions
         mergefa   merge two FASTA/Q files
         famask    apply a X-coded FASTA to a source FASTA
         dropse    drop unpaired from interleaved PE FASTA/Q
         rename    rename sequence names
         randbase  choose a random base from hets
         cutN      cut sequence at long N
         listhet   extract the position of each het
==============================================================

$seqtk seq

Usage:   seqtk seq [options] <in.fq>|<in.fa>

Options: -q INT    mask bases with quality lower than INT [0] #将质量小于INT的碱基，转成小写的字母[atgc]，INT默认是0。
         -X INT    mask bases with quality higher than INT [255] #标记质量大于INT的碱基。INT默认是255
         -n CHAR   masked bases converted to CHAR; 0 for lowercase [0]#用给出的CHAR字符代替标记的碱基，0表示用原碱基的小写字母表示。默认为0。这个参数应该和-q 或-X 搭配使用
         -l INT    number of residues per line; 0 for 2^32-1 [0] #每条序列取前INT个碱基。默认为0，表示保留整条序列
         -Q INT    quality shift: ASCII-INT gives base quality [33]#质量变换，如ASCII-33
         -s INT    random seed (effective with -f) [11]#随机种子，配合-f参数，默认11
         -f FLOAT  sample FLOAT fraction of sequences [1]#随机取整个文件的FLOAT（例如：0.5）行，随机数种子由-s决定。默认为1，表示保留所有序列
         -M FILE   mask regions in BED or name list FILE [null]#FILE可以是BED文件。若是BED文件，就将BED文件中给定区间的碱基转换成小写[atgc]序列；若是列表文件，则屏蔽掉给定的ID对应的整条序列。默认为空
         -L INT    drop sequences with length shorter than INT [0]#丢弃掉长度小于INT的序列，默认是0
         -F CHAR   fake FASTQ quality []# 用CHAR字符替换fq的质量值
         -c        mask complement region (effective with -M)# 标记互补区域，和-M参数配合使用
         -r        reverse complement#生成反向互补序列
         -A        force FASTA output (discard quality)#强制转换成fa格式，也可以用-a
         -C        drop comments at the header lines#在标题行删除注释
         -N        drop sequences containing ambiguous bases#丢弃掉含有不确定碱基N的序列
         -1        output the 2n-1 reads only#仅输入2n-1（奇数）的reads
         -2        output the 2n reads only#仅输入2n-1（偶数）的reads
         -V        shift quality by '(-Q) - 33' #通过-Q-33转换质量值
         -U        convert all bases to uppercases#所有碱基换成大写字母
         -S        strip of white spaces in sequences#删除序列中的空白行

$seqtk sample 

Usage:   seqtk sample [-2] [-s seed=11] <in.fa> <frac>|<number>
#随机抽取序列，用法是seqtk sample fq/fa num

Options: -s INT       RNG seed [11]#设置随机种子，默认11
         -2           2-pass mode: twice as slow but with much reduced memory#占用更大的内存

$seqtk subseq

Usage:   seqtk subseq [options] <in.fa> <in.bed>|<name.list>
#提取name.list中指定名称的fa序列，
Options: -t       TAB delimited output# 输出以tab分割
         -l INT   sequence line length [0]# 输出序列以长度INT换行

Note: Use 'samtools faidx' if only a few regions are intended.#注意：如果只有少数几个区域，请使用'samtools faidx'

$seqtk mergepe
Usage: seqtk mergepe <in1.fq> <in2.fq>
# 交叉合并双端测序的序列，pe就是pair end的意思

$seqtk trimfq

Usage:   seqtk trimfq [options] <in.fq>

Options: -q FLOAT    error rate threshold (disabled by -b/-e) [0.05]#设置错误率的阈值为FLOAT，以此作为修剪标准。此参数不可与-b/-e参数同时使用。默认值为0.05
         -l INT      maximally trim down to INT bp (disabled by -b/-e) [30]#无论是否质量低，序列保留到至少INT长度。此参数不可与-b/-e参数同时使用。默认值为30。此参数可以看下图（R2.fastq有三条read，测序质量依次递增）
         -b INT      trim INT bp from left (non-zero to disable -q/-l) [0]# 从序列左边切除INT个碱基。此参数不可与-q/-l参数同时使用。默认值为0
         -e INT      trim INT bp from right (non-zero to disable -q/-l) [0]#从序列右边切除INT个碱基。此参数不可与-q/-l参数同时使用。默认值为0
         -L INT      retain at most INT bp from the 5'-end (non-zero to disable -q/-l) [0]#保留从5'端起前INT个碱基
         -Q          force FASTQ output#强制输出fq格式

$seqtk mergefa
Usage: seqtk mergefa [options] <in1.fa> <in2.fa># 合并两个的FASTA/Q files
Options: -q INT   quality threshold [0]
         -i       take intersection#取交集
         -m       convert to lowercase when one of the input base is N
         -r       pick a random allele from het
         -h       suppress hets in the input

$seqtk rename #序列重命名
Usage: seqtk rename <in.fq> [prefix]

$seqtk cutN# 在N长度处切掉序列

Usage:   seqtk cutN [options] <in.fa>

Options: -n INT    min size of N tract [1000]
         -p INT    penalty for a non-N [10]
         -g        print gaps only, no sequence

作者：一只烟酒僧
链接：https://www.jianshu.com/p/8d032a29d5a1
来源：简书
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