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 代码运行次数:0 运行 AI代码解释 git clone https://github.com/lh3...
out.fastq4.截取序列 切除reads的前5bp,以及后10bp: seqtk trimfq -b 5 -e 10 in.fq > out.fq 使用Phred算法从两端修剪低质量的碱基: seqtk trimfq in.fq > out.fq 5.得到fastq/fasta 文件的碱基组成 seqtk comp input.fastq > out.txt
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.
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 hety regional heterozygosity # 区域性杂合 gc identify high...
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...
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 ...
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 ...
fastq Where, input.fasta or input.fastq are the name of your input FASTA/FASTQ files, and ids.txt contains the list of sequences IDs (one ID per line) to extract from the FASTA/FASTQ files.The ids.txt can also contains the sequence ID and specific sequence regions, similar to three ...
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 ...
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. To installseqtk, git clone https://github.com/lh3/seqtk.git;cdseqtk;make ...