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metagenomics [2021/03/17 13:09] – external edit 127.0.0.1metagenomics [2022/07/07 10:30] (current) – ↷ Links adapted because of a move operation 207.46.13.204
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   * [[http://www.metagenomics.wiki/|Metagenomics wiki]]   * [[http://www.metagenomics.wiki/|Metagenomics wiki]]
   * [[http://blog.mothur.org/2016/01/12/mothur-and-qiime/|mothur and QIIME]] Despite their differences in philosophy, //most// of the differences in mothur and QIIME are cosmetic.   * [[http://blog.mothur.org/2016/01/12/mothur-and-qiime/|mothur and QIIME]] Despite their differences in philosophy, //most// of the differences in mothur and QIIME are cosmetic.
 +  * [[https://youtu.be/ED8VkMLYTTI|Aligning 16S sequences to reference set and filtering the alignment]] This tutorial explains how to align 16S sequences to the Silva reference set and how to filter the alignment and remove identical sequences.
  
 ===== 16S rRNA-based ===== ===== 16S rRNA-based =====
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 GroopM, a companion of CheckM, can be used to recover genomes from metagenomic data.[[https://peerj.com/articles/603/|논문]] GroopM, a companion of CheckM, can be used to recover genomes from metagenomic data.[[https://peerj.com/articles/603/|논문]]
  
 +===== Shotgun metagenomic analysis 2022 =====
 +최근 들어서 입수한 메타게놈 자료의 분석을 위하여 새롭게 글 작성을 시작한다. 오래 전에 작성했던 위 내용의 해당 섹션을 보충하느니 차라리 새로운 섹션을 만들고, 필요하다면 별도의 위키 문서로 독립하는 것이 나을 것이다. Biostars에 실린 최근 질문과 답변(2022년 1월 20일 기준 4개월 전)이 훌륭한 시작점이 될 것이다.
 +
 +[[https://www.biostars.org/p/9488577/|Any suggestions on metagenomic pipelines for processing shotgun metagenomics whole genome sequencing samples?]] - metaWRAP, bioBakery & anvi'o
 +
 +Shotgun metagenomic analysis라고 하여 반드시 MAG(metagenome-assembled genome)을 중간물로 사용하는 것은 아니다. 예를 들어 마커 유전자 DB를 이용한 정밀한 phylogenetic analysis라면, read를 꼭 조립해야 하는 것은 아니기 때문이다.
 +
 +[[metagenomic_data_assembly_pipeline]]
  
  
metagenomics.1615954153.txt.gz · Last modified: 2021/03/17 13:09 by 127.0.0.1