fasta/fastq文件处理的瑞士军刀-seqtk

阿凡亮

发布于 2020-04-14 09:10:52

2.3K0

发布于 2020-04-14 09:10:52

文章被收录于专栏：生物信息学生物信息学

引言

上次在只用一行颠覆你处理文件的方式里面说了可以用Seqtk来处理fasta/fastq文件。那么这一期就来讲讲怎么来使用seqtk。

Seqtk简介及安装

Seqtk是Heng Li(https://github.com/lh3)大神开发的一款用于处理fasta/fastq文件的工具，因其操作轻便且跨平台，继而受到广大科研人员的青睐，目前这个项目在github上已经被标星602次。Seqtk的安装就和Heng Li大神的图像一样简单

git clone https://github.com/lh3/seqtk.git;cd seqtk; make

这样seqtk的二进制文件就生成了。

Seqtk有几个常用的子命令

seq 就是最常用的子命令了

> seqtk seqUsage: seqtk seq [options] <in.fq>|<in.fa>Options: -q INT 将测序质量小于INT的碱基变成小写（默认为0） -X INT 测序质量大于INT的碱基变成小写（默认为255） -n CHAR 满足-q或-X条件下的碱基都被转成CHAR字符 -l INT 每一行碱基的数量，最大为2^32-1 -Q INT 测序质量在不同测序平台中的质量偏移量（默认为33） -s INT 随机种子（默认为11） -f FLOAT 随机取用户提供比例的子序列（默认是全部序列） -M FILE 用BED格式或含有序列名的文件来将所选序列变成小写 -L INT 丢弃长度小于一定长度的序列 -c 互补 -r 反向互补 -A 强制将序列转化为FASTA格式 -C 去掉文件头中的注释行 -N 去掉含有不确定碱基的行 -1 输出奇数行的reads -2 输出偶数行的reads -V 通过'(-Q) - 33'来改变质量值 -U 将所有的碱基变成大写 -S 去掉序列里面的空白

我们可以将fastq文件长序列折叠成多行短序列（-l），反向互补(-r)，并生成fasta文件(-A)

> head -8 test.fq@A00679:63:HGVWCDSXX:4:1271:5927:18176CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCAAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF@A00679:63:HGVWCDSXX:4:2461:25970:10614CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCTAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF
# 用60bp的长度对序列进行折叠> seqtk seq -l 60 -r -A test.fq | head -8>A00679:63:HGVWCDSXX:4:1271:5927:18176GCAGCAATGGCGGCCCGCCCCGTTGTTTGAGTCACGGCAACAACGGCCGCCTCCGTCGCGAAAACCGCAGCAACAGAGCCGCCTCTAACTCTCTGGCTCAACCGCCGCCGCCGCCTTGGCCGGCACAACGCGACTAGCGTCATCTCAACG>A00679:63:HGVWCDSXX:4:2461:25970:10614GCAGCAATGGCGGCCCGCCCCGTTGTTTGAGTCACGGCAACAACGGCCGCCTCCGTCGCGAAAACCGCAGCAACAGAGCCGCCTCTAACTCTCTGGCTCAACCGCCGCCGCCGCCTAGGCCGGCACAACGCGACTAGCGTCATCTCAACG

过滤掉长度小于一定长度的序列(-L)，并将质量值小于一定值的碱基进行mask(-q)，并生成fasta文件(-A)

# 质量值小于20的碱基都变成了小写，长度小于100bp的序列不会被输出> seqtk seq -L 100 -q 20 test.fq | head -8@A00679:63:HGVWCDSXX:4:1271:5927:18176CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCAAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF@A00679:63:HGVWCDSXX:4:2461:25970:10614CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCTAGGCGGCGGCGGCGGTTGAGCCAGaGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF@A00679:63:HGVWCDSXX:4:1625:12680:18912GCGGtTTTCGCGACGGAGGCGGCcGTTgTTGCCGaGACTCAAACAACggGgCGGGCCgCCATTGCtgCTCACgCTGCCGAGCAGCTTCCGCGATCAAgGATGCaGGCCgCCAtCGACGCCTCCgTaGCCGCtGACCtgGgAGAGgGATGG+:FFF,FFF:FFF:FF:FFFFFFF,:F:,FFFFF:,:FF:FFFFFFFF,,F,F:FFFF,FFFFFFF,,F:FFF,FFFFF:FFFFFFFFFFFFFFFFFF,FFFFF,FFFF,FFF,FFFF:FFFFF,F,FFFFF,FFFF,,F,F:FF,FF:FF

sample 使用随机种子（-s，保证重复性）提取一定比例（0.4）的子序列

# 以10为种子，提取全部序列的40%> seqtk sample -s 10 test.fq 0.4@A00679:63:HGVWCDSXX:4:1271:5927:18176CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCAAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF@A00679:63:HGVWCDSXX:4:2461:25970:10614CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCTAGGCGGCGGCGGCGGTTGAGCCAGaGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF@A00679:63:HGVWCDSXX:4:1625:12680:18912GCGGtTTTCGCGACGGAGGCGGCcGTTgTTGCCGaGACTCAAACAACggGgCGGGCCgCCATTGCtgCTCACgCTGCCGAGCAGCTTCCGCGATCAAgGATGCaGGCCgCCAtCGACGCCTCCgTaGCCGCtGACCtgGgAGAGgGATGG+:FFF,FFF:FFF:FF:FFFFFFF,:F:,FFFFF:,:FF:FFFFFFFF,,F,F:FFFF,FFFFFFF,,F:FFF,FFFFF:FFFFFFFFFFFFFFFFFF,FFFFF,FFFF,FFF,FFFF:FFFFF,F,FFFFF,FFFF,,F,F:FF,FF:FF

comp 如果你想知道每条序列的碱基组成这个命令你一定会使用的。而且支持使用bed文件（-r），对子序列进行查看。

> cat test.bedA00679:63:HGVWCDSXX:4:1625:12680:18912	4	30# 结果里面的列含义分别为：chr, length, #A, #C, #G, #T, #2, #3, #4, #CpG, #tv, #ts, #CpG-ts> seqtk comp -r test.bed test.fqA00679:63:HGVWCDSXX:4:1625:12680:18912	4	30	2	6	10	8	00	0	10	0	0	0

subseq 如果你只想提取某几条序列/或者某一段区间里的序列，那么就可以使用这个命令；也可以指定一行输出（-t）

> echo "A00679:63:HGVWCDSXX:4:1403:24569:25911" | seqtk subseq -t test.fq -@A00679:63:HGVWCDSXX:4:1403:24569:25911ATTCACTCATGTACACCTTTCTTCCTCCTCTCTTCATCTCCTATCCCAAATATCTATCTCAACCATCTACATGGCTTCATCTCCTCCTTTGTTCCCGTCGTCCGATCCATTTGCTATCTTAGCCTTAGCTAGCTAGCTAGGGTTTCTTGA+FFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF:FFFFFFF::F::FFFFFF::FF:FFFFFFF:FFFF:F:FFFFF:F:F:FFFFFFFFFFFFFFF,:FF,FFF,,FFF,,FFFFFFFF> echo "A00679:63:HGVWCDSXX:4:1403:24569:25911" | seqtk subseq -t test.fq -A00679:63:HGVWCDSXX:4:1403:24569:25911	1	ATTCACTCATGTACACCTTTCTTCCTCCTCTCTTCATCTCCTATCCCAAATATCTATCTCAACCATCTACATGGCTTCATCTCCTCCTTTGTTCCCGTCGTCCGATCCATTTGCTATCTTAGCCTTAGCTAGCTAGCTAGGGTTTCTTGA

fqchk 查看每个碱基位点在不同序列上的碱基分布情况，错误率，质量值等

> seqtk fqchk test.fqmin_len: 150; max_len: 150; avg_len: 150.00; 3 distinct quality valuesPOS	#bases	%A	%C	%G	%T	%N	avgQ	errQ	%low	%highALL	900	15.2	31.0	31.3	22.4	0.0	35.2	24.3	4.2	95.81	6	16.7	33.3	50.0	0.0	0.0	35.0	31.6	0.0	100.02	6	0.0	50.0	33.3	16.7	0.0	37.0	37.0	0.0	100.03	6	0.0	33.3	16.7	50.0	0.0	37.0	37.0	0.0	100.04	6	0.0	16.7	16.7	66.7	0.0	35.0	31.6	0.0	100.05	6	16.7	0.0	33.3	50.0	0.0	30.7	18.6	16.7	83.36	6	33.3	16.7	33.3	16.7	0.0	37.0	37.0	0.0	100.07	6	33.3	0.0	33.3	33.3	0.0	37.0	37.0	0.0	100.08	6	33.3	16.7	0.0	50.0	0.0	37.0	37.0	0.0	100.09	6	16.7	16.7	33.3	33.3	0.0	35.0	31.6	0.0	100.010	6	0.0	0.0	83.3	16.7	0.0	37.0	37.0	0.0	100.011	6	33.3	50.0	16.7	0.0	0.0	37.0	37.0	0.0	100.012	6	0.0	33.3	50.0	16.7	0.0	37.0	37.0	0.0	100.0...149	6	0.0	0.0	100.0	0.0	0.0	37.0	37.0	0.0	100.0150	6	16.7	33.3	50.0	0.0	0.0	37.0	37.0	0.0	100.0

mergepe 通常我们Illunima双端测序会得到两个文件R1.fq.gz和R2.fq.gz，这个命令就是帮助怎么完美实现两两配对

> cat test.1.fq@A00679:63:HGVWCDSXX:4:1101:2392:1438 1:N:0:CCTTAATA+CCTTAATCCGGCGGGCGCATCGTGGTGGGCTGCATCCCGTACCGCGTGCGGTGCGACGGCGAGCTGGAGGTGCTGGCGATCACGTCCCAGAAGGGGCACGGCATGATGTTCCCCAAGGGCGGGTGGGAGGTGGACGAGTCCATGGACGAGGCCGCCA+FFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@A00679:63:HGVWCDSXX:4:1101:5285:1438 1:N:0:CCTTAATA+CCTTAATCCTGGGCTTTCTGATGGTCCTCCCAAGCCTGGATCTTGATCTCTTCTCGCTTGAATCTCGCTAATTACTTGGCCGTCTCCGCCTCCTCCCACGCAGCCGCACGGATCGCGGTTATGTTCTGCGTCGACTGGTCCATGGGCACCGGTTTCA+,FFFFF,:F:F:F::FFFFFFF::FFF,FF:,FFF,:FFF:FFFFFFFFFF:F:FFFFFF,FF,,FFFFFF,F:,FFF,,FFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFF:FFFF:F:FF:F:F,FF,FF,FFFF:,F,@A00679:63:HGVWCDSXX:4:1101:12391:1438 1:N:0:CCTTAATA+CCTTAATAGGGGTGGATTGAGAGTGCCTCATCCTATCTGAAGCCCTAATGAAGAGTGAGACTATTCTTGGAGCTGCTCCTACACCATAAAGTGGTGGGATGCTCATTGTAAACCAATGTCCCATCAATGCTTGGAAGGGCTGCACACTTTCAGCACG+FFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFF:FFFFF:FFFFFFFF:FFF:FFFF::FFFF,FFFFFFFF
> cat test.2.fq@A00679:63:HGVWCDSXX:4:1101:2392:1438 2:N:0:CCTTAATA+CCTTAATGCTCGACGAGCCGCTCCAGCGCCTCGCGCATCCACCAGTGCGGGCACCCGTCCATCACCTGCTGCACCGTTGCCCAGGTGCGCTTGCGGGACGCCATCTCGGGCCACTGGTGGAGCTCGTCGGCGACGCGGAGCGGGAACATGAACCCCT+FFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFF,FFFFF,FFFFF@A00679:63:HGVWCDSXX:4:1101:5285:1438 2:N:0:CCTTAATA+CCTTAATGCAAGCCAAGAGCCGTCCCGGACCGGGACGCCGGTGAGGGCGACGAGCCCAAACTGCTCCCAGCCAACGACTCCACGGAGGACGCTCGGTGGCCCCAGCGCAGTCGGCTCCTTCATCAGCCACGGCGGAGAATGCAGCAGCTCGGAGCTG+:FFFFFFFF:FF::FFFFFFFF:FFFFFFFFFF::FFFFFF:FFFFFFFFFFFFFFFFF,FF:FFFFF:FFF:,FFFFFFF::FFFFF,FF:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF:,,FFFF:FFFFFF:FF:FFFFFFFFF@A00679:63:HGVWCDSXX:4:1101:12391:1438 2:N:0:CCTTAATA+CCTTAATTCCTGTCATACTAATATCTTTGTTTCTGGCGATAACACGGAACAGTCGTAGTGGCTTTAGACTACTATGGTACTAGCAAAGAATTGAAAATGTCAAGTGGCTGTAGAGATATTGCAATACGAAAGGTAGCTGTTCATAATGTAGAAATCA+FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFF,FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFF
# 使用mergepe以后，序列A00679:63:HGVWCDSXX:4:1101:2392:1438的R1和R2就并到一起了> seqtk mergepe test.1.fq test.2.fq | head -8@A00679:63:HGVWCDSXX:4:1101:2392:1438 1:N:0:CCTTAATA+CCTTAATCCGGCGGGCGCATCGTGGTGGGCTGCATCCCGTACCGCGTGCGGTGCGACGGCGAGCTGGAGGTGCTGGCGATCACGTCCCAGAAGGGGCACGGCATGATGTTCCCCAAGGGCGGGTGGGAGGTGGACGAGTCCATGGACGAGGCCGCCA+FFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@A00679:63:HGVWCDSXX:4:1101:2392:1438 2:N:0:CCTTAATA+CCTTAATGCTCGACGAGCCGCTCCAGCGCCTCGCGCATCCACCAGTGCGGGCACCCGTCCATCACCTGCTGCACCGTTGCCCAGGTGCGCTTGCGGGACGCCATCTCGGGCCACTGGTGGAGCTCGTCGGCGACGCGGAGCGGGAACATGAACCCCT+FFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFF,FFFFF,FFFFF

trimfq 通常序列两端会出现质量相对较低的情况，这个时候为了序列高质量，需要对序列进行修剪（-b 5'端的碱基，-e 3'端的碱基）

> head -8 test.fq@A00679:63:HGVWCDSXX:4:1271:5927:18176CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCAAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF@A00679:63:HGVWCDSXX:4:2461:25970:10614CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCTAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF
# 5'端剪切30bp碱基，3'端剪切30bp碱基> seqtk trimfq -b 30 -e 30 test.fq | head -8@A00679:63:HGVWCDSXX:4:1271:5927:18176GCCAAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGAC+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@A00679:63:HGVWCDSXX:4:2461:25970:10614GCCTAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGAC+FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

rename 在每条序列的名称前面加上前缀

> seqtk rename test.fq test_prefix | head -8@test_prefix1CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCAAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF@test_prefix2CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCTAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF

cutN 去掉序列中的N/或者查看N所在的位置信息（-n 指定N的最小长度）

> head -8 testN.fa>A00679:63:HGVWCDSXX:4:1271:5927:18176CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCNNNNCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTNNNNNNNTCGCGACGGAGGCGGCCGTTGTTGCCGTGACTCAAACAACGGGGCGGGCCGCCATTGCTGC>A00679:63:HGVWCDSXX:4:2461:25970:10614CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCTAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTGNNNNNACTCAAACAACGGGGCGGGCCGCCATTGCTGC>A00679:63:HGVWCDSXX:4:1625:12680:18912GCGGTTTTCGCGACGGAGGCGGCCGTTGTTGCCGAGACTCAAACAACGGGGCGGGCCGCCATTGCTGCTCACGCTGCCGAGCAGCTTCCGCGATCAAGGATGCAGGCCGCCATCGACGCCTCCGTAGCCGCTGACCTGGGAGAGGGATGG>A00679:63:HGVWCDSXX:4:1329:18557:30592GCCTTGATGGCGTCGGCATCCCCATCCGCCGCCGGCGACGACATCTCTCCCTGCACTGTTGCCATGTCCGCCTTCCGATGGCTATGCTGCGCTGCCGACGACGGGTCGGCCAGTAACAGTAACTGTCGCAACGGGATGCGCGAGCTGTGG
# 指定N的最小长度为1，然后输出N在序列中的坐标> seqtk cutN -n 1 -g testN.faA00679:63:HGVWCDSXX:4:1271:5927:18176	33	37A00679:63:HGVWCDSXX:4:1271:5927:18176	82	89A00679:63:HGVWCDSXX:4:2461:25970:10614	113	118

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原始发表：2019-12-07，如有侵权请联系 cloudcommunity@tencent.com 删除

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