seqtk使用

seqtk安装和使用 ------------------------------
Nickier
2018-12-13
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1.下载

conda search seqtk conda install -y seqtk

2.查看seqtk的子命令
$seqtk Usage:seqtk Version: 1.3-r106Command: seqcommon transformation of FASTA/Q # FASTA/Q 的转换 compget the nucleotide composition of FASTA/Q # 获取FASTA/Q的核苷酸组成 samplesubsample sequences # 获取样本序列 subseqextract subsequences from FASTA/Q # 提取子序列 fqchkfastq QC (base/quality summary) # fastq的质控 mergepeinterleave two PE FASTA/Q files #交叉合并双端测序的两个FASTA/Q files,合并后的file第一条序列是第一个fq的第一条,合并后的file第二条是序列是第二个fq的第一条 trimfqtrim FASTQ using the Phred algorithm # 用Phred算法对fq修剪hetyregional heterozygosity # 区域性杂合 gcidentify high- or low-GC regions# 识别高低GC含量的区域 mutfapoint mutate FASTA at specified positions#在特定位置指出FASTA的突变 mergefamerge two FASTA/Q files # 合并两个的FASTA/Q files famaskapply a X-coded FASTA to a source FASTA#将X编码的fa应用到原fa dropsedrop unpaired from interleaved PE FASTA/Q# 从交错合并的fa/fq中丢弃不成对的序列 renamerename sequence names#序列重命名 randbasechoose a random base from hets#从hets中随机选一个碱基 cutNcut sequence at long N # 在N长度处切掉序列 listhetextract the position of each het #提取每一个het位置

3.命令 3.1 seqtk seq
$seqtk seqUsage:seqtk seq [options] |Options: -q INTmask 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 INTmask bases with quality higher than INT [255] #标记质量大于INT的碱基。INT默认是255 -n CHARmasked 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 INTnumber 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 INTquality shift: ASCII-INT gives base quality [33]#质量变换,如ASCII-33 -s INTrandom seed (effective with -f) [11]#随机种子,配合-f参数,默认11 -f FLOATsample 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 FILEmask 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 INTdrop sequences with length shorter than INT [0]#丢弃掉长度小于INT的序列,默认是0 -F CHARfake FASTQ quality []# 用CHAR字符替换fq的质量值 -cmask complement region (effective with -M)# 标记互补区域,和-M参数配合使用 -rreverse complement#生成反向互补序列 -Aforce FASTA output (discard quality)#强制转换成fa格式,也可以用-a -Cdrop comments at the header lines#在标题行删除注释 -Ndrop sequences containing ambiguous bases#丢弃掉含有不确定碱基N的序列 -1output the 2n-1 reads only#仅输入2n-1(奇数)的reads -2output the 2n reads only#仅输入2n-1(偶数)的reads -Vshift quality by '(-Q) - 33' #通过-Q-33转换质量值 -Uconvert all bases to uppercases#所有碱基换成大写字母 -Sstrip of white spaces in sequences#删除序列中的空白行

-q将质量小于INT的碱基,转成小写的字母[atgc],INT默认是0。

seqtk使用
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-q.png -q 和-n
seqtk使用
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-n.png 【seqtk使用】-r生成反向互补序列
seqtk使用
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-r.png 3.2 seqtk comp
$seqtk comp Usage:seqtk comp [-u] [-r in.bed] # 获取fa的碱基的组成信息,用-r参数可以输出bed中的给定区间的序列Output format: chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts # 输出格式:序列号序列长度ACGT

seqtk使用
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comp.png 3.3 seqtk sample
$seqtk sample Usage:seqtk sample [-2] [-s seed=11] | #随机抽取序列,用法是seqtk sample fq/fa numOptions: -s INTRNG seed [11]#设置随机种子,默认11 -22-pass mode: twice as slow but with much reduced memory#占用更大的内存

3.4 seqtk subseq
$seqtk subseqUsage:seqtk subseq [options] | #提取name.list中指定名称的fa序列, Options: -tTAB delimited output# 输出以tab分割 -l INTsequence 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使用
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subseq.png 3.5 seqtk fqchk
$seqtk fqchk Usage: seqtk fqchk [-q 20] #获取每个碱基点的分布和质量值,和fastqc质控类似,不过这里生成的是数据,而fastqc生成质控报告 Note: use -q0 to get the distribution of all quality values#用-q0来获取所有质量值的分布

seqtk使用
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fqchk.png 3.6 seqtk mergepe
$seqtk mergepe Usage: seqtk mergepe # 交叉合并双端测序的序列,pe就是pair end的意思

3.7 seqtk trimfq
$seqtk trimfqUsage:seqtk trimfq [options] Options: -q FLOATerror 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 INTmaximally 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 INTtrim 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 INTtrim 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 INTretain 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 -Qforce FASTQ output#强制输出fq格式

seqtk使用
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trimfq.png 3.8 seqtk hety
$seqtkhetyUsage:seqtk hety [options] #区域性杂合Options: -w INTwindow size [50000] -t INT# start positions in a window [5] -mtreat lowercases as masked

3.9 seqtk gc
$seqtk gc Usage: seqtk gc [options] # 识别高低GC含量的区域 Options: -widentify high-AT regions -f FLOATmin GC fraction (or AT fraction for -w) [0.60] -l INTmin region length to output [20] -x FLOATX-dropoff [10.0]

3.10 seqtk mutfa
$seqtk mutfa Usage: seqtk mutfa #给定in.snp特定位置指出fa的突变Note: contains at least four columns per line which are: 'chr1-based-posanybase-changed-to'.

3.11 seqtk mergefa
$seqtk mergefaUsage: seqtk mergefa [options] # 合并两个的FASTA/Q filesOptions: -q INTquality threshold [0] -itake intersection#取交集 -mconvert to lowercase when one of the input base is N -rpick a random allele from het -hsuppress hets in the input

3.12 seqtk famask
$seqtk famask# 将X编码的fa应用到原fa Usage: seqtk famask

3.13 seqtk dropse
$seqtk dropse# 从交叉合并的fa/fq中丢弃不成对的序列 Usage: seqtk dropse

3.14 seqtk rename
$seqtk rename #序列重命名 Usage: seqtk rename [prefix]

3.15 seqtk randbase
$seqtk randbase#从hets中随机选一个碱基 Usage: seqtk randbase

3.16 seqtk cutN
$seqtk cutN# 在N长度处切掉序列Usage:seqtk cutN [options] Options: -n INTmin size of N tract [1000] -p INTpenalty for a non-N [10] -gprint gaps only, no sequence

3.17 seqtk listhet
$seqtk listhet #提取每一个het位置 Usage: seqtk listhet

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