seqkit rename: new flag-s/--separatorfor setting separator between original ID/name and the counter (default "_").#360 new flag-N/--start-numfor setting starting count number for duplicated IDs/names (default 2).#360 new flag-1/--rename-1st-recfor renaming the first record as well.#...
rename-重新命名重复的IDrestart-为环状基因组重新设置起始位置concat-将多个文件中含有相同的ID的序列连接成一条序列mutate-编辑序列(点突,插入,删除)6)排序sort-按照id/name/sequence进行排序2、具体用法。添加环境变量(添加到自己的.bashrc,别忘了source):export PATH=path:$PATH1)序列操作。seqkit seq [flags] ...
samplesample sequences by number or proportion headprint first N FASTA/Q records Edit replacereplace name/sequence by regular expression renamerename duplicated IDs Ordering shuffleshuffle sequences sortsort sequences by id/name/sequence Misc
5.随机抽取序列,按照比例或者数量 -s设定随机种子,便于重复 seqtk sample -s 10 test.fq 0.4 #比例seqtk sample -s 10 test.fq 100 #数量 6.重命名 会将序列id变为从1到n... seqtk rename in.fa <前缀> > out.fa 7..fastq转换为fasta,支持压缩格式 seqtk seq -a in.fq.gz > out.fa.gz 8.使...
编辑和排序：replace修改序列，rename重命名，sort进行序列排序。 具体用法：通过添加环境变量调用，如`export PATH=path:$PATH`，并参照各种命令的参数选项进行操作，例如`seqkit seq -w 100 test.fa`以100碱基为行输出序列。例如，对文件进行长度统计和筛选特定序列：- seqkit fx2tab -l -g -n -i...
For example, to unify names of protein with unknown functions, we want to rename "hypothetical" to "putative" in lower case. The replacing rules are listed below in tab-delimited file:$ cat changes.tsv Hypothetical putative hypothetical putative Putative putative ...
seqkit rename: rename ID only, do not append original header to new ID. #236 seqkit fx2tab: for -s/--seq-hash: outputing MD5 instead of hash value (integers) of xxhash. #219 Bugfixes seqkit seq: fix failing to output gzipped format for file name with extension of .gz since ...
sekqit rename consumes too much memory. I've improved it (seqkit_linux_amd64.tar.gz). A lot of R2 reads failed to pass the fastp, 1.7G-910M, it's a big number so seqkit pair need a lot of memory to buffer these SE R1 reads. Another low-memory method: Still call seqkit rename...
replace replace name/sequence by regular expression rename rename duplicated IDsOrderingshuffle shuffle sequences sort sort sequences by id/name/sequenceMiscversion print version information and check for update Technical details and guides for useFASTA/Q format parsing...