(base)bio03@VM-0-6-ubuntu:~/opt/bin$ seqkit seqkit:command not found(base)bio03@VM-0-6-ubuntu:~/opt/bin$./seqkit # 使用./+软件名称可以调看详情和运行 SeqKit--a cross-platform and ultrafast toolkitforFASTA/Qfile manipulation Version:0.15.0Author:WeiShen<shenwei356@gmail.com>Documents:...
The problem is that Filtlong does not allow duplicated read IDs and apparently, some were found in my data. I have searched for ways to remove duplicates in a big fastq file and I have found seqkit and the rmdup command. I first used the following command : zcat ./fastq/all_fastq.trimm...
002、解压 tar -xzvf seqkit_linux_amd64.tar.gz 003、调用测试 ./seqkit --help | head
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print("Warning %i IDs not found in %s" % (len(wanted) - count, fastafile)) if __name__ == '__main__': main() 另存为get_seqs_by_id.py 使用方法: python get_seqs_by_id.py -f **.fasta -i ID.txt -o out_file.fasta ...
do not remove embeded regions when searching with regular expressions.#368 seqkit amplicon: fix BED coordinates for amplicons found in the minus strand.#367 seqkit split: fix forgetting to add extension for--two-pass.#332 seqkit stats:
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Long-option version of the command:$ seqkit fx2tab --name --only-id --alphabet viral.1.1.genomic.fna.gz \ | csvtk --no-header-row --tabs grep --fields 4 --use-regexp --ignore-case --pattern "[^ACGT]" You can then exclude these sequences with seqkit grep:...
seqkit pair: fix a dangerous bug: when input files are not in current directory, input files were overwritten.SeqKit v0.16.0 - 2021-04-16 new command seqkit head-genome: print sequences of the first genome with common prefixes in name seqkit grep/locate/amplicon -m much faster (300...