在Windows系统中安装并使用seqkit工具

seqkit软件介绍: Seqkit是一款专门处理fsata/q序列文件的软件,由go语言编写,功能比较完善,软件使用也很稳定。 下载链接:https://bioinf.shenwei.me/seqkit/download/ 下载方式: 1. 点...

seqkit软件介绍:

Seqkit是一款专门处理fsata/q序列文件的软件,由go语言编写,功能比较完善,软件使用也很稳定。

下载链接https://bioinf.shenwei.me/seqkit/download/

下载方式

1. 点击下载到本地(任意地址)attachments-2024-03-3Xnm6DaG65f94e57b2069.png

2. For windows, just copy seqkit.exe to C:\WINDOWS\system32.将下载的seqkit.exe软件复制到本地C:\Windows\System32中

attachments-2024-03-RFQKyppQ65f94f0d894b1.png运行软件:

1. 打开windows系统的Windows power shell页面。输入命令:seqkit version。确认是否下载安装成功:

attachments-2024-03-jlim1YCo65f94fd6ec01e.png2. 之后就可以使用seqkit工具处理生信文件了。

seqkit工具的命令如下:

Compression level:
  format   range   default  comment
  gzip     1-9     5        https://github.com/klauspost/pgzip sets 5 as the default value.
  xz       NA      NA       https://github.com/ulikunitz/xz does not support.
  zstd     1-4     2        roughly equals to zstd 1, 3, 7, 11, respectively.
  bzip     1-9     6        https://github.com/dsnet/compress
Usage:
  seqkit [command]
Commands for Basic Operation:
  faidx           create the FASTA index file and extract subsequences
  scat            real time recursive concatenation and streaming of fastx files
  seq             transform sequences (extract ID, filter by length, remove gaps, reverse complement...)
  sliding         extract subsequences in sliding windows
  stats           simple statistics of FASTA/Q files
  subseq          get subsequences by region/gtf/bed, including flanking sequences
  translate       translate DNA/RNA to protein sequence (supporting ambiguous bases)
  watch           monitoring and online histograms of sequence features
Commands for Format Conversion:
  convert         convert FASTQ quality encoding between Sanger, Solexa and Illumina
  fa2fq           retrieve corresponding FASTQ records by a FASTA file
  fq2fa           convert FASTQ to FASTA
  fx2tab          convert FASTA/Q to tabular format (and length, GC content, average quality...)
  tab2fx          convert tabular format to FASTA/Q format
Commands for Searching:
  amplicon        extract amplicon (or specific region around it) via primer(s)
  fish            look for short sequences in larger sequences using local alignment
  grep            search sequences by ID/name/sequence/sequence motifs, mismatch allowed
  locate          locate subsequences/motifs, mismatch allowed
Commands for Set Operation:
  common          find common/shared sequences of multiple files by id/name/sequence
  duplicate       duplicate sequences N times
  head            print first N FASTA/Q records
  head-genome     print sequences of the first genome with common prefixes in name
  pair            match up paired-end reads from two fastq files
  range           print FASTA/Q records in a range (start:end)
  rmdup           remove duplicated sequences by ID/name/sequence
  sample          sample sequences by number or proportion
  split           split sequences into files by id/seq region/size/parts (mainly for FASTA)
  split2          split sequences into files by size/parts (FASTA, PE/SE FASTQ)
Commands for Edit:
  concat          concatenate sequences with the same ID from multiple files
  mutate          edit sequence (point mutation, insertion, deletion)
  rename          rename duplicated IDs
  replace         replace name/sequence by regular expression
  restart         reset start position for circular genome
  sana            sanitize broken single line FASTQ files
Commands for Ordering:
  shuffle         shuffle sequences
  sort            sort sequences by id/name/sequence/length
Commands for BAM Processing:
  bam             monitoring and online histograms of BAM record features
Commands for Miscellaneous:
  merge-slides    merge sliding windows generated from seqkit sliding
  sum             compute message digest for all sequences in FASTA/Q files
Additional Commands:
  genautocomplete generate shell autocompletion script (bash|zsh|fish|powershell)
  version         print version information and check for update
Flags:
      --alphabet-guess-seq-length int   length of sequence prefix of the first FASTA record based on
                                        which seqkit guesses the sequence type (0 for whole seq)
                                        (default 10000)
      --compress-level int              compression level for gzip, zstd, xz and bzip2. type "seqkit -h"
                                        for the range and default value for each format (default -1)
  -h, --help                            help for seqkit
      --id-ncbi                         FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2|
                                        Pseud...
      --id-regexp string                regular expression for parsing ID (default "^(\\S+)\\s?")
  -X, --infile-list string              file of input files list (one file per line), if given, they are
                                        appended to files from cli arguments
  -w, --line-width int                  line width when outputting FASTA format (0 for no wrap) (default 60)
  -o, --out-file string                 out file ("-" for stdout, suffix .gz for gzipped out) (default "-")
      --quiet                           be quiet and do not show extra information
  -t, --seq-type string                 sequence type (dna|rna|protein|unlimit|auto) (for auto, it
                                        automatically detect by the first sequence) (default "auto")
  -j, --threads int                     number of CPUs. can also set with environment variable
                                        SEQKIT_THREADS) (default 4)
Use "seqkit [command] --help" for more information about a command.




  • 发表于 2024-03-19 17:01
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  • 分类:软件工具

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