Usage:seqkit rmdup[flags]Flags:-n,--by-name by full name instead of just id-s,--by-seq by seq-D,--dup-num-filestringfile to save number and list of duplicated seqs-d,--dup-seqs-filestringfile to save duplicated seqs-h,--help helpforrmdup-i,--ignore-caseignorecase sample zcat hai...
将fastq转换成fasta: seqtk seq -a Sample_R1.fq.gz > Sample_R1.fa 得到反向互补序列: seqtk seq -r Sample_R1.fq.gz > Sample_Revc_R1.fq 2.sample 随机抽样 seqtk sample -s100 Sample_R1.fq.gz 10000 #可直接对压缩文件进行序列随机提取,在提取R1和R2两个文件的时候,需要-s值一致,才能使提取...
seqtk sample -s 10 test.fq 0.4 #比例 seqtk sample -s 10 test.fq 100 #数量6.重命名 会将序列id变为从1到n...seqtk rename in.fa <前缀> > out.fa7..fastq转换为fasta,支持压缩格式seqtk seq -a in.fq.gz > out.fa.gz8.使用Phred算法从两端修剪低质量的碱基:seqtk trimfq in.fq > out....
$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 numOptions:-s INT RNG seed[11]#设置随机种子,默认11-22-passmode:twiceasslow butwithmuch reduced memory#占用更大的内存 ...
sample subsample sequences # 获取样本序列 subseq extract subsequencesfromFASTA/Q# 提取子序列 fqchk fastqQC(base/quality summary)# fastq的质控 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, ...
sample subsample sequences# 获取样本序列 subseq extract subsequences from FASTA/Q# 提取子序列 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, ...
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 代码语言:javascript 复制 #以10为种子,提取全部序列的40%>seqtk sample-s10test.fq0.4@A00679:63:HGVWCDSXX:4:1271:5927:18176CGTTGAGATGACGCTAGTCGCGTTGTGCCGGCCAAGGCGGCGGCGGCGGTTGAGCCAGAGAGTTAGAGGCGGCTCTGTTGCTGCGGTTTTCGCGACGGAGGCGGCCGTTGTTG...
sample subsample sequences # 获取样本序列 subseq extract subsequences from FASTA/Q # 提取子序列 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, ...
seqtk sample -s100 read1.fq 10000 > sub1.fq seqtk sample -s100 read2.fq 10000 > sub2.fq -s后面跟随机seed,对于双端测序的reads,必须使用一样的seed,不然得到的sample无法正确pair 对fq/fa文件中的reads进行开头/末尾的trim seqtk trimfq -b 5 -e 10 in.fa > out.fa ...
sample subsample sequences# 获取样本序列 subseq extract subsequences from FASTA/Q# 提取子序列 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, ...