metagenomics
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metagenomics [2018/04/06 10:40] – [Phylogenetic classification of contigs] hyjeong | metagenomics [2022/07/07 10:30] (current) – ↷ Links adapted because of a move operation 207.46.13.204 | ||
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====== Haeyoung' | ====== Haeyoung' | ||
- | ===== Useful papers | + | ===== Useful papers, websites, and videos |
* [[https:// | * [[https:// | ||
* [[https:// | * [[https:// | ||
* [[http:// | * [[http:// | ||
* [[http:// | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[http:// | ||
+ | * [[https:// | ||
===== 16S rRNA-based ===== | ===== 16S rRNA-based ===== | ||
==== QiiME ==== | ==== QiiME ==== | ||
* http:// | * http:// | ||
- | * [[https:// | + | * [[https://docs.qiime2.org/2019.1/|Qiime 2 user documentation]] |
* [[http:// | * [[http:// | ||
+ | * [[https:// | ||
* [[https:// | * [[https:// | ||
* [[https:// | * [[https:// | ||
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* [[http:// | * [[http:// | ||
* [[http:// | * [[http:// | ||
+ | ==== Mothur ==== | ||
+ | * https:// | ||
+ | ==== Others ==== | ||
+ | * [[16S rRNA sequencing data types]] | ||
+ | * [[custom scripts for 16S rRNA sequence analysis]] | ||
===== Taxonomic profiling from metagenomic shotgun sequences (without assembly) ==== | ===== Taxonomic profiling from metagenomic shotgun sequences (without assembly) ==== | ||
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CONCOCT, MaxBin, metaBAT... | CONCOCT, MaxBin, metaBAT... | ||
- | ===== Pipelines for metagenomc data analysis ===== | + | ===== Pipelines |
* MetAMOS [[https:// | * MetAMOS [[https:// | ||
* MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis [[https:// | * MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis [[https:// | ||
+ | * MicrobiomeAnalysis - a web-based tool for comprehensive statistical, | ||
===== A real example of Cyanobacterial genome assembly ===== | ===== A real example of Cyanobacterial genome assembly ===== | ||
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GroopM, a companion of CheckM, can be used to recover genomes from metagenomic data.[[https:// | GroopM, a companion of CheckM, can be used to recover genomes from metagenomic data.[[https:// | ||
+ | ===== 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:// | ||
+ | |||
+ | Shotgun metagenomic analysis라고 하여 반드시 MAG(metagenome-assembled genome)을 중간물로 사용하는 것은 아니다. 예를 들어 마커 유전자 DB를 이용한 정밀한 phylogenetic analysis라면, | ||
+ | |||
+ | [[metagenomic_data_assembly_pipeline]] | ||
metagenomics.1522978819.txt.gz · Last modified: 2021/03/17 13:09 (external edit)