seqtk trimfq in.fq > out.fq 注:seqtk对于一些不涉及测序质量的处理,通常都是既支持fasta格式,也支持fastq格式
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 代码语言:javascript 复制 git clone https://github.com/lh3/seqtk.git;cd seqtk;make ...
5.得到fastq/fasta 文件的碱基组成 seqtk comp input.fastq > out.txt # input.fastq文件 >NB001 GGGGTTTTGTGCAT #out.txt 输出内容 NB001 14 6 6 1 1 0 0 0 0 0 0 0 6.合并两个序列 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 $seqtkm...
seqtk 一款快速处理fasta/fastq 文件的小程序 seqtk 的 GitHub 官网 https://github.com/lh3/seqtk 安装 git clone https://github.com/lh3/seqtk.gitcd seqtkmakeThe only library dependency is zlib.
famask apply a X-codedFASTAto a sourceFASTAdropse drop unpairedfrominterleavedPEFASTA/Qrename rename sequence names randbase choose a randombasefromhets cutN cut sequence atlongNlisthet extract the position of each het seqtk的使用 以fastq格式文件Akle_TTAGGC_L004_R1_001.fastq.gz为例 ...
mergepe interleave twoPEFASTA/Qfiles # 交叉合并双端测序的两个FASTA/Qfiles, # 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 trimfq trimFASTQusing the Phred algorithm # 用Phred算法对fq修剪 ...
1.将fastq 文件转换成fasta 文件 seqtk seq -A input.fastq > output.fasta 2.得到反向互补序列 seqtk seq -Ar input.fastq > output.fasta 3.seqtk comp: 得到fastq/fasta 文件的碱基组成 (输出格式:序列id 序列长度 A C G T ) seqtk comp in.fa > out.fa ...
Convert FASTQ to FASTA: seqtkseq-a in.fq.gz > out.fa Convert ILLUMINA 1.3+ FASTQ to FASTA and mask bases with quality lower than 20 to lowercases (the 1st command line) or toN(the 2nd): seqtkseq-aQ64 -q20 in.fq > out.fa ...
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. Seqtk Examples Convert FASTQ to FASTA: seqtk seq -a in.fq.gz > out.fa ...
fqchk fastq QC (base/quality summary) # fastq的质控 mergepe interleave 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 trimfq trim FASTQ using the Phred algorithm # 用Phred算法对...