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blast
Introduction

简介

BLAST(Basic Local Alignment Search Tool)是生物序列相似性比较及区域查找的分析工具。可用于推断序列之间的功能和进化关系，以及帮助鉴定基因家族的成员。

该BLAST WDL 工作流程采用 ncbi-BLAST+ 2.13.0 软件
其主要包括以子程序：

  • blastp：蛋白序列与蛋白库做比对。
  • blastx：核酸序列对蛋白库的比对。
  • blastn：核酸序列对核酸库的比对。
  • tblastn：蛋白序列对核酸库的比对，将给定的氨基酸序列与核酸数据库中的序列（双链）按不同的阅读框进行比对。
  • tblastx: 核酸序列对核酸库的比对，检索的序列和核酸序列数据库中的序列按不同的阅读框全部翻译成蛋白质序列，然后进行蛋白质序列比对。

可以通过method参数切换不同子程序，默认 为blastn。

BLAST详细说明请查阅NCBI 说明文档

使用案例

1.使用预设BLAST Database

目前该流程收纳了CNGBdb新冠数据库数据，未来我们会收纳更多CNGBdb归档数据，您可以配置通过 input 中dbname 参数，选择不同数据库。

2. 自定义BLAST Database

你可以通过 File 类型参数 custom_db 及 String 类型参数 custom_db_dbtype 分别定义您需要检索自定义数据库序列文件和文件类型。

除此之外，我们支持用户个性化修改不同子程序的默认参数，从而达到理想的结果。

如：修改Task name 中 blast.runtblastn 的 Attribute name 为word_size即修改blast工作流中blastn中特异的word_size 参数。

详细参数介绍查看下文input参数。

联系我们

该工具由计算平台团队提供。如有任何问题或疑虑，请联系CNGBdb@cngb.org

Script
Input
Task nameAttribute nameTypeDescription
*
      blast
    queryfaFile
      Input file name
    
*
      blast.runtblastx
    word_sizeInt
      Word size for wordfinder algorithm (length of best perfect match)
    
*
      blast.runtblastx
    taxidsString
      Restrict search of database to include only the specified taxonomy IDs(multiple IDs delimited by ',')
    
*
      blast.runtblastx
    segString
      Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)
    
*
      blast.runtblastx
    negative_taxidsString
      Restrict search of database to everything except the specified taxonomy IDs
    
*
      blast.runtblastx
    max_target_seqsInt
      Maximum number of aligned sequences to keep
    
*
      blast.runtblastx
    max_hspsInt
      Set maximum number of HSPs per subject sequence to save for each query
    
*
      blast.runtblastx
    matrixString
      Scoring matrix name (normally BLOSUM62)
    
*
      blast.runtblastx
    lcase_maskingBoolean
      Use lower case filtering in query and subject sequence(s)?
    
*
      blast.runtblastn
    word_sizeInt
      Word size for wordfinder algorithm (length of best perfect match)
    
*
      blast.runtblastn
    taxidsString
      Restrict search of database to include only the specified taxonomy IDs(multiple IDs delimited by ',')
    
*
      blast.runtblastn
    segString
      Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)
    
*
      blast.runtblastn
    negative_taxidsString
      Restrict search of database to everything except the specified taxonomy IDs
    
*
      blast.runtblastn
    max_target_seqsInt
      Maximum number of aligned sequences to keep
    
*
      blast.runtblastn
    max_hspsInt
      Set maximum number of HSPs per subject sequence to save for each query
    
*
      blast.runtblastn
    matrixString
      Scoring matrix name (normally BLOSUM62)
    
*
      blast.runtblastn
    lcase_maskingBoolean
      Use lower case filtering in query and subject sequence(s)?
    
*
      blast.runtblastn
    gapopenInt
      Cost to open a gap
    
*
      blast.runtblastn
    gapextendInt
      Cost to extend a gap
    
*
      blast.runtblastn
    comp_based_statsString
      Use composition-based statistics: D or d: default (equivalent to 2 ) ;0 or F or f: No composition-based statistics;1: Composition-based statistics as in NAR 29:2994-3005, 2001;2 or T or t : Composition-based score adjustment as in Bioinformatics;3: Composition-based score adjustment as in Bioinformatics 21:902-911
    
*
      blast.runblastx
    word_sizeInt
      Word size for wordfinder algorithm (length of best perfect match)
    
*
      blast.runblastx
    taxidsString
      Restrict search of database to include only the specified taxonomy IDs(multiple IDs delimited by ',')
    
*
      blast.runblastx
    segString
      Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)
    
*
      blast.runblastx
    negative_taxidsString
      Restrict search of database to everything except the specified taxonomy IDs
    
*
      blast.runblastx
    max_target_seqsInt
      Maximum number of aligned sequences to keep
    
*
      blast.runblastx
    max_hspsInt
      Set maximum number of HSPs per subject sequence to save for each query
    
*
      blast.runblastx
    matrixString
      Scoring matrix name (normally BLOSUM62)
    
*
      blast.runblastx
    lcase_maskingBoolean
      Use lower case filtering in query and subject sequence(s)?
    
*
      blast.runblastx
    gapopenInt
      Cost to open a gap
    
*
      blast.runblastx
    gapextendInt
      Cost to extend a gap
    
*
      blast.runblastx
    comp_based_statsString
      Use composition-based statistics: D or d: default (equivalent to 2 ) ;0 or F or f: No composition-based statistics;1: Composition-based statistics as in NAR 29:2994-3005, 2001;2 or T or t : Composition-based score adjustment as in Bioinformatics;3: Composition-based score adjustment as in Bioinformatics 21:902-911
    
*
      blast.runblastp
    word_sizeInt
      Word size for wordfinder algorithm (length of best perfect match)
    
*
      blast.runblastp
    taxidsString
      Restrict search of database to include only the specified taxonomy IDs(multiple IDs delimited by ',')
    
*
      blast.runblastp
    segString
      Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable)
    
*
      blast.runblastp
    negative_taxidsString
      Restrict search of database to everything except the specified taxonomy IDs
    
*
      blast.runblastp
    max_target_seqsInt
      Maximum number of aligned sequences to keep
    
*
      blast.runblastp
    max_hspsInt
      Set maximum number of HSPs per subject sequence to save for each query
    
*
      blast.runblastp
    matrixString
      Scoring matrix name (normally BLOSUM62)
    
*
      blast.runblastp
    lcase_maskingBoolean
      Use lower case filtering in query and subject sequence(s)?
    
*
      blast.runblastp
    gapopenInt
      Cost to open a gap
    
*
      blast.runblastp
    gapextendInt
      Cost to extend a gap
    
*
      blast.runblastp
    comp_based_statsString
      Use composition-based statistics: D or d: default (equivalent to 2 ) ;0 or F or f: No composition-based statistics;1: Composition-based statistics as in NAR 29:2994-3005, 2001;2 or T or t : Composition-based score adjustment as in Bioinformatics;3: Composition-based score adjustment as in Bioinformatics 21:902-911
    
*
      blast.runblastn
    word_sizeInt
      Word size for wordfinder algorithm (length of best perfect match)
    
*
      blast.runblastn
    taxidsString
      Restrict search of database to include only the specified taxonomy IDs(multiple IDs delimited by ',')
    
*
      blast.runblastn
    tasksString
      Task to execute
    
*
      blast.runblastn
    strandString
      Query strand(s) to search against database/subject
    
*
      blast.runblastn
    rewardInt
      Reward for a nucleotide match
    
*
      blast.runblastn
    penaltyInt
      Penalty for a nucleotide mismatch
    
*
      blast.runblastn
    negative_taxidsString
      Restrict search of database to everything except the specified taxonomy IDs
    
*
      blast.runblastn
    max_target_seqsInt
      Maximum number of aligned sequences to keep
    
*
      blast.runblastn
    max_hspsInt
      Set maximum number of HSPs per subject sequence to save for each query
    
*
      blast.runblastn
    lcase_maskingBoolean
      Use lower case filtering in query and subject sequence(s)?
    
*
      blast.runblastn
    gapopenInt
      Cost to open a gap
    
*
      blast.runblastn
    gapextendInt
      Cost to extend a gap
    
*
      blast.runblastn
    dustString
      Filter query sequence with DUST (Format: 'yes', 'level window linker', or 'no' to disable)
    
*
      blast
    threadsInt
      Number of threads (CPUs) to use in the BLAST search
    
*
      blast
    outfmtInt
      alignment view options
    
*
      blast
    methodString
      Blast component :blastn blastp blastx tblastn tblasx
    
*
      blast
    dbnameString
      path of blast database by CNGBdb team provided
    
*
      blast
    evalueFloat
      Expectation value (E) threshold for saving hits
    
*
      blast
    blast_docker_overrideString
      docker of blast software
    
*
      blast
    custom_dbFile
      User-defined file of blast database 
    
*
      blast
    custom_db_dbtypeFile
      data type of user-defined file of blast database 
    
Output
Task nameAttribute nameTypeDescription
*
      blast
    fina_outputFile
      Return the output file to the column name of the corresponding table by this.xxx